The Base quality option doesn't seem to apply to modded machines. eg Bobs Mods Electronics Assembly Machines, or Electrolyzers, or Bucket Wheel Excavators. AMS seems to be partial. Electric Mining Drill will have it, but Bobs Drill 2/3 or Large mining Drill does not. But Bobs Distillery, chemical furnace, and metal mixing furnaces do have an AMS option. Again bucket wheel excavators do not have AMS options.

Deadlocks stacking beltboxes have AMS and quality baseline and probably shouldn't (loop cheating).

I see... The stacking beltboxes are technically furnaces (any crafting machine that behaves like a furnace) and that's why it triggers AMS and base quality additions. However, due to the nature of how the beltboxes are made, the fix for that specific problem will be on their end. I'll make a PR.
I don't have any idea why some of the other machines you mentioned don't have base quality or AMS versions.

Should be fixed now in the latest 1.3.8 version, other than the beltboxes which are waiting on a fix from their side.