Here is the full 'udevadm test' output for two disks on the same port
multiplier channel. I can do a disk on a different channel as well if
you want.

On 12.04, the sysfs path of the same disk slot is
/sys/devices/pci0000:00/0000:00:01.0/0000:01:00.0/0000:02:00.0/host8/target8:0:0/8:0:0:0/block/sdk
(the sdN numbering is inconsistent from boot to boot, which is why we
want /dev/disk/by-path names for all of them). We don't have any 14.04
hosts with a port multiplier, so I don't know when the kernel started
putting the hostN directory in the /ataN/ directory and thus triggering
udev's special ATA disk handling.

('udevadm test /sys/class/block/sdk' on the 12.04 machine says that udev
sees this as an ATA and SATA disk; ID_ATA and ID_ATA_SATA are both 1 and
ID_BUS is ata. But it winds up with
ID_PATH=pci-0000:02:00.0-scsi-2:0:0:0, instead of an ata variant.)

I agree with your analysis that this is affects systemd HEAD. As far as
I can see HEAD has nothing in handle_scsi_ata() that would give
different names to multiple disks behind the same ATA port. Sadly we
have no systems that are running a recent enough systemd that I can
report it to them, based on their reporting policies. Is there a
bootable live CD of the in-progress next Ubuntu versions? That might
have a recent enough systemd that I could boot it on the system in
question, verify that its systemd isn't generating the right /dev/disk
/by-path results, and report it upstream.

** Attachment added: "full-out"
   
https://bugs.launchpad.net/ubuntu/+source/systemd/+bug/1611945/+attachment/4719114/+files/full-out

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https://bugs.launchpad.net/bugs/1611945

Title:
  /dev/disk/by-path not properly populated for (e)SATA port multiplier
  disks

Status in systemd package in Ubuntu:
  New

Bug description:
  We have a just-installed Ubuntu 16.04 LTS machine with a number of
  disks behind port-multiplier eSATA ports, all of them driven by a SiI
  3124 controller (sata_sil24 kernel driver). Our machine sees all disks
  on all channels, however under 16.04 only one disk from each channel
  shows up in /dev/disk/by-path/ (all disks show up in /dev/disk/by-id
  and /dev/disk/by-uuid). For our usage this is a severe defect because
  we rotate disks in and out of the external enclosure and rely on
  mounting specific slots in the external enclosure through /dev/disk
  /by-path.

  This did not happen in Ubuntu 12.04 LTS, the release that this machine
  was previously running.

  According to 'udevadm info --export-db' and 'udevadm test-builtin
  path_id' and so on, systemd's udev stuff is assigning all drives
  behind the same port the same disk/by-path data (ID_PATH et al). In
  'udevadm info /sys/block/sdX', the 'P:' and 'E: DEVPATH=' values show
  a difference in the target portion of PCI path, eg:

    P: 
/devices/pci0000:00/0000:00:01.0/0000:01:00.0/0000:02:00.0/ata1/host0/target0:0:0/0:0:0:0/block/sda
    P: 
/devices/pci0000:00/0000:00:01.0/0000:01:00.0/0000:02:00.0/ata1/host0/target0:1:0/0:1:0:0/block/sdb

  However the 'S: disk/by-path', 'E: DEVLINKS=', and 'E: ID_PATH'
  portions do not. For both devices above, we see:

    S: disk/by-path/pci-0000:02:00.0-ata-1
    E: ID_PATH=pci-0000:02:00.0-ata-1

  Naturally only one device can have a /dev/disk/by-
  path/pci-0000:02:00.0-ata-1 symlink, so instead of four disks per
  channel in /dev/disk/by-path we see one.

  Ubuntu release: 16.04

  Package versions from 'apt-cache policy udev systemd':
  udev:
    Installed: 229-4ubuntu7
  systemd:
    Installed: 229-4ubuntu7

  'journalctl -b' reports that during boot systemd does report some
  'appeared twice with different sysfs paths' notes, eg:

  Aug 10 13:34:21 verdandi systemd[1]: dev-disk-by\x2dpath-
  pci\x2d0000:02:00.0\x2data\x2d1\x2dpart1.device: Dev dev-disk-by
  \x2dpath-pci\x2d0000:02:00.0\x2data\x2d1\x2dpart1.device appeared
  twice with different sysfs paths
  
/sys/devices/pci0000:00/0000:00:01.0/0000:01:00.0/0000:02:00.0/ata1/host0/target0:3:0/0:3:0:0/block/sdd/sdd1
  and
  
/sys/devices/pci0000:00/0000:00:01.0/0000:01:00.0/0000:02:00.0/ata1/host0/target0:0:0/0:0:0:0/block/sda/sda1

  However it doesn't seem to be reporting this for all port-multiplier
  drives and their partitions.

  If it would be useful I can attach full 'udevadm info --export-db'
  output or the like.

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