A: We agree on that. Simple, the solution (patch) is on hd-idle sourceforge. That's unrelated to autoshutdown.
B: Indeed hdparm.conf is not to make changes. But you can read the file and verify. Changes made in APM in GUI affect this file.
I had trouble with the setting up hd-idle: The guide says make sure APM is turned off. First option in APM is "Disabled", last one is "255 - Disabled".
Not all 6 data drives (not all the same drives, Samsung and WD) were spinning down, I was reading at the hdparm man pages about the 255 option. Since I set "255 - Disabled" for each drive in APM (GUI), they all appeared in hdparm.conf like this:
apm = 255
write_cache = on
After, all drives were spinning down.
I haven't read all of your posts, but I though the more info the better and tried to help by sharing my experience.
If write cache if off (it should be for SSD's) and APM is set "Disabled" (as default, first option) the drive does not appear in hdparm.conf (also other options not used, automatic acoustic management and spin-down time).
Don't know the cause of your hd-idle-restart-resume.service not working stable. But I does in my case (also using autoshutdown now). Maybe the APM set to 255 is a solution, maybe not use backport but install like you did here or maybe DO use option C. Things to try I would say...