As an engineer used to reading technical standards, this is my 2c...
Firstly, it seems there is nothing new here at all in terms of the requirements! You can roll back the standard five years online and the wording is identical. The requirements themselves look pretty ancient in fact - I've had cars over 20 years old with window systems that seem designed around exactly those or very similar requirements, e.g. needing ignition on, or ignition off but before you open the door, or continuous button press, etc. Note the wording Tesla uses in their message - 'due to recent federal regulations'. Cheeky! Implying new regulations without actually saying 'new', because they aren't new!
The requirements themselves:
S4 gives specific circumstances under which the windows can be closed - e.g. manually, with ignition on, continuous remote button press etc. Under these circumstances you wouldn't even need an auto stop and reverse safety feature
S5 essentially says 'or, you can close a window however and whenever you want provided it has an auto stop and reverse feature that meets the following requirements...'
Tesla (and other manufacturers) systems like close on lock (without continuous press), close from app, etc do not fall under the circumstances of S4, therefore they are relying on an auto stop and reverse feature complying with S5.
So it's reasonably clear that all that has happened here is that Tesla's auto stop and reverse feature has found to be non-compliant with S5. They tried to fix it with an update, but that has not worked and so now they have to disable those features that do not fall under S4.