OK, this improves things slightly; the first timeout is gone:

[    0.124444] kernel: pci 0000:07:00.1: Linked as a consumer to 0000:07:00.0
[    0.124592] kernel: PCI: CLS 64 bytes, default 64
[    0.124621] kernel: Unpacking initramfs...

But the second (longer) timeout is still there, and now has a trace:

[    4.601812] kernel: usb 1-7: New USB device strings: Mfr=0, Product=0, 
SerialNumber=0
[   28.016007] kernel: watchdog: BUG: soft lockup - CPU#4 stuck for 23s! 
[swapper/0:1]
[   28.016007] kernel: Modules linked in:
[   28.016007] kernel: CPU: 4 PID: 1 Comm: swapper/0 Not tainted 
5.0.0-16-generic #17~lp1830905+2
[   28.016007] kernel: Hardware name: Gigabyte Technology Co., Ltd. B450M 
DS3H/B450M DS3H-CF, BIOS F4 01/25/2019
[   28.016007] kernel: RIP: 0010:xhci_reset+0x7f/0x1a0
[   28.016007] kernel: Code: 00 00 00 4d 8b 6c 24 18 bb 80 96 98 00 eb 17 a8 02 
74 43 bf c7 10 00 00 e8 4e 30 25 00 83 eb 01 0f 84 e9 00 00 00 41 8b 45 00 <83> 
f8 ff 75 e0 b8 ed ff ff ff 5b 41 5c 41 5d 5d c3 48 8b 07 48 c7
[   28.016007] kernel: RSP: 0018:ffffacb30004bad0 EFLAGS: 00000202 ORIG_RAX: 
ffffffffffffff13
[   28.016007] kernel: RAX: 0000000000000002 RBX: 0000000000050ef2 RCX: 
0000000000000002
[   28.016007] kernel: RDX: 00000000000013d4 RSI: 00000024d0b051d8 RDI: 
0000000000000ded
[   28.016007] kernel: RBP: ffffacb30004bae8 R08: 00000000ffffffff R09: 
0000000000000000
[   28.016007] kernel: R10: 0000000000000002 R11: 000000000000000f R12: 
ffff89803bf62230
[   28.016007] kernel: R13: ffffacb302480020 R14: ffffffff8bbddee0 R15: 
ffff89803bf62230
[   28.016007] kernel: FS:  0000000000000000(0000) GS:ffff89804eb00000(0000) 
knlGS:0000000000000000
[   28.016007] kernel: CS:  0010 DS: 0000 ES: 0000 CR0: 0000000080050033
[   28.016007] kernel: CR2: 00007f3995075e04 CR3: 00000001ec00e000 CR4: 
00000000003406e0
[   28.016007] kernel: Call Trace:
[   28.016007] kernel:  xhci_gen_setup+0x224/0x3e0
[   28.016007] kernel:  ? pci_bus_read_config_byte+0x40/0x60
[   28.016007] kernel:  xhci_pci_setup+0x56/0x120
[   28.016007] kernel:  usb_add_hcd+0x2cb/0x8a0
[   28.016007] kernel:  usb_hcd_pci_probe+0x283/0x480
[   28.016007] kernel:  xhci_pci_probe+0x30/0x230
[   28.016007] kernel:  local_pci_probe+0x47/0xa0
[   28.016007] kernel:  pci_device_probe+0x145/0x1b0
[   28.016007] kernel:  really_probe+0xfe/0x3f0
[   28.016007] kernel:  ? set_debug_rodata+0x17/0x17
[   28.016007] kernel:  driver_probe_device+0x11a/0x130
[   28.016007] kernel:  __driver_attach+0xe3/0x110
[   28.016007] kernel:  ? driver_probe_device+0x130/0x130
[   28.016007] kernel:  ? driver_probe_device+0x130/0x130
[   28.016007] kernel:  bus_for_each_dev+0x74/0xb0
[   28.016007] kernel:  ? kmem_cache_alloc_trace+0x1a6/0x1c0
[   28.016007] kernel:  driver_attach+0x1e/0x20
[   28.016007] kernel:  bus_add_driver+0x167/0x260
[   28.016007] kernel:  ? xhci_debugfs_create_root+0x25/0x25
[   28.016007] kernel:  driver_register+0x60/0x100
[   28.016007] kernel:  ? xhci_debugfs_create_root+0x25/0x25
[   28.016007] kernel:  __pci_register_driver+0x5a/0x60
[   28.016007] kernel:  xhci_pci_init+0x47/0x49
[   28.016007] kernel:  do_one_initcall+0x4a/0x1c9
[   28.016007] kernel:  kernel_init_freeable+0x1cb/0x272
[   28.016007] kernel:  ? rest_init+0xb0/0xb0
[   28.016007] kernel:  kernel_init+0xe/0x110
[   28.016007] kernel:  ret_from_fork+0x22/0x40
[   28.874267] kernel: xhci_hcd 0000:07:00.2: can't setup: -110
[   28.874275] kernel: xhci_hcd 0000:07:00.2: USB bus 3 deregistered
[   28.874312] kernel: xhci_hcd 0000:07:00.2: init 0000:07:00.2 fail, -110
[   28.874314] kernel: xhci_hcd: probe of 0000:07:00.2 failed with error -110

I've done a bit of digging regarding the USB bus; I believe it's present
to support a USB-C port which some RTX 2060 cards do have, but my
specific model _does not_ have.

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https://bugs.launchpad.net/bugs/1830905

Title:
  Nvidia RTX 2060 USB bus timeouts cause ~30s delay in boot

Status in linux package in Ubuntu:
  Confirmed

Bug description:
  From dmesg:

  [    0.132667] kernel: pci 0000:07:00.1: Linked as a consumer to 0000:07:00.0
  [    5.882727] kernel: pci 0000:07:00.2: xHCI HW not ready after 5 sec (HC 
bug?) status = 0x801
  [    5.882781] kernel: pci 0000:07:00.2: quirk_usb_early_handoff+0x0/0x6a6 
took 5615333 usecs

  <snip>

  [    9.984204] kernel: usb 1-7: new full-speed USB device number 4 using 
xhci_hcd
  [   10.308689] kernel: usb 1-7: New USB device found, idVendor=8087, 
idProduct=0a2b, bcdDevice= 0.10
  [   10.308690] kernel: usb 1-7: New USB device strings: Mfr=0, Product=0, 
SerialNumber=0
  [   34.654721] kernel: xhci_hcd 0000:07:00.2: can't setup: -110
  [   34.654730] kernel: xhci_hcd 0000:07:00.2: USB bus 3 deregistered
  [   34.654769] kernel: xhci_hcd 0000:07:00.2: init 0000:07:00.2 fail, -110
  [   34.654771] kernel: xhci_hcd: probe of 0000:07:00.2 failed with error -110

  $ lspci -k -s 0000:07:00
  07:00.0 VGA compatible controller: NVIDIA Corporation TU106 [GeForce RTX 2060 
Rev. A] (rev a1)
        Subsystem: Gigabyte Technology Co., Ltd TU106
        Kernel driver in use: nvidia
        Kernel modules: nvidiafb, nouveau, nvidia_drm, nvidia
  07:00.1 Audio device: NVIDIA Corporation TU106 High Definition Audio 
Controller (rev a1)
        Subsystem: Gigabyte Technology Co., Ltd TU106 High Definition Audio 
Controller
        Kernel driver in use: snd_hda_intel
        Kernel modules: snd_hda_intel
  07:00.2 USB controller: NVIDIA Corporation TU106 USB 3.1 Host Controller (rev 
a1)
        Subsystem: Gigabyte Technology Co., Ltd TU106 USB 3.1 Host Controller
  07:00.3 Serial bus controller [0c80]: NVIDIA Corporation TU106 USB Type-C 
Port Policy Controller (rev a1)
        Subsystem: Gigabyte Technology Co., Ltd TU106 USB Type-C Port Policy 
Controller
        Kernel driver in use: nvidia-gpu
        Kernel modules: i2c_nvidia_gpu

  ProblemType: Bug
  DistroRelease: Ubuntu 19.10
  Package: linux-image-5.0.0-15-generic 5.0.0-15.16
  ProcVersionSignature: Ubuntu 5.0.0-15.16-generic 5.0.6
  Uname: Linux 5.0.0-15-generic x86_64
  NonfreeKernelModules: nvidia_modeset nvidia
  ApportVersion: 2.20.11-0ubuntu2
  Architecture: amd64
  AudioDevicesInUse:
   USER        PID ACCESS COMMAND
   /dev/snd/controlC0:  daniel     4470 F.... pulseaudio
   /dev/snd/controlC1:  daniel     4470 F.... pulseaudio
   /dev/snd/controlC2:  daniel     4470 F.... pulseaudio
  CurrentDesktop: i3
  Date: Wed May 29 09:36:51 2019
  InstallationDate: Installed on 2019-05-07 (21 days ago)
  InstallationMedia: Ubuntu 18.04.2 LTS "Bionic Beaver" - Release amd64 
(20190210)
  MachineType: Gigabyte Technology Co., Ltd. B450M DS3H
  ProcFB: 0 EFI VGA
  ProcKernelCmdLine: BOOT_IMAGE=/vmlinuz-5.0.0-15-generic 
root=/dev/mapper/ubuntu--vg-root ro quiet splash 
resume=UUID=73909634-a75d-42c9-8f66-a69138690756 vt.handoff=1
  RelatedPackageVersions:
   linux-restricted-modules-5.0.0-15-generic N/A
   linux-backports-modules-5.0.0-15-generic  N/A
   linux-firmware                            1.179
  SourcePackage: linux
  UpgradeStatus: Upgraded to eoan on 2019-05-08 (20 days ago)
  dmi.bios.date: 01/25/2019
  dmi.bios.vendor: American Megatrends Inc.
  dmi.bios.version: F4
  dmi.board.asset.tag: Default string
  dmi.board.name: B450M DS3H-CF
  dmi.board.vendor: Gigabyte Technology Co., Ltd.
  dmi.board.version: x.x
  dmi.chassis.asset.tag: Default string
  dmi.chassis.type: 3
  dmi.chassis.vendor: Default string
  dmi.chassis.version: Default string
  dmi.modalias: 
dmi:bvnAmericanMegatrendsInc.:bvrF4:bd01/25/2019:svnGigabyteTechnologyCo.,Ltd.:pnB450MDS3H:pvrDefaultstring:rvnGigabyteTechnologyCo.,Ltd.:rnB450MDS3H-CF:rvrx.x:cvnDefaultstring:ct3:cvrDefaultstring:
  dmi.product.family: Default string
  dmi.product.name: B450M DS3H
  dmi.product.sku: Default string
  dmi.product.version: Default string
  dmi.sys.vendor: Gigabyte Technology Co., Ltd.

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