One shot focus calibration and AFMA deal with issues with the steps a lens takes on the camera used,
No, steps are small compared to the thinnest DOF. The best way to think of body calibration and AF MA is as an offset to the BFCVs.
with manual focus and focus trap there is no such thing.
It doesn't matter how the subject comes into focus (AF, MF, or change in camera-to-subject distance), confirmation is the same independent process with the same behaviour (including interrogating the lens for BFCVs, which are not available from an adapter chip).
Only issues with parts of the light spectrum the AF sensor is sensitive to not all focussing on the same plane (spherical aberrations, LoCA, sensitivity to IR and UV (which depends on camera model)) can plague certain lenses concerning focus confirmation.
You can't rely on getting accurate focus confirmation if you don't have good BFCVs (except by luck), and those chips can't deliver them.
Even AI-Servo and One shot focus with focus confirmation can deliver different results.
Different in what way?
One shot focus does not check if focus is reached.
It does in all cases apart from one rare one.
AI-Servo constantly looks if something is in focus or not.
Yep, it's the same process as One-shot but One-shot stops when focus is confirmed.
Did you try to read the rest?
I succeeded.

But it was irrelevant to what I'm talking about so I didn't address it.
Focus trap and manual focus focus confirmation images taken with various adapted lenses with various focus confirmation chips, on Canon EOS 450D and Canon EOS 6D:
Sure, you can get lucky, I never said you couldn't.
--
Check out the unofficial
Rebel Talk FAQ. Sorry it's out of date, but DPReview still won't allow us to edit our articles.