>> so I still have to wire the card to the motherboard's CD-in
connector, and get the sound from ALSA's CD input channel.

try

options snd-hda-intel model=6stack-digout


use  line in instead of CD 

or

use hdajackretask or early patching to set node 0x1c to CD  to get CD
playback volume/switch at node 0x0b


Node 0x0b [Audio Mixer] wcaps 0x20010b: Stereo Amp-In
  Amp-In caps: ofs=0x23, nsteps=0x41, stepsize=0x03, mute=1
  Amp-In vals:  [0x80 0x80] [0x80 0x80] [0x80 0x80] [0x80 0x80] [0xaa 0xaa] 
[0xa3 0xa3] [0x80 0x80] [0x80 0x80]
  Connection: 8
     0x18 0x19 0x1a 0x1b 0x1c 0x1d 0x14 0x15

Node 0x1c [Pin Complex] wcaps 0x400001: Stereo
  Pincap 0x00000020: IN
  Pin Default 0x00000000: [Jack] Line Out at Ext N/A
    Conn = Unknown, Color = Unknown
    DefAssociation = 0x0, Sequence = 0x0
  Pin-ctls: 0x00:

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https://bugs.launchpad.net/bugs/566381

Title:
  Lag when using module-loopback

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