I work for a tiny company, just 2 of us writing the software, myself and my manager who infrequently looks over my code. If I'd try to write something directly manipulating registers I'd be told to do it again using the HAL functions.
FYI, sooner or later you
will encounter the situation that you simply cannot get a working solution by only using the "HAL functions" - some are simply completely broken, some are slightly buggy and require workarounds, some are too slow due to bloat and cannot be used in, for example, interrupt services. And some just are not flexible enough as-is to provide the features the chip datasheet advertised.
When you hit this scenario, you have the following options (I've seen exactly this):
1) Just make the code work and pretend you have followed the insane rules,
1a) If your boss finds out and is sensible, they'll pretend you followed the rules as well,
1b) If your boss finds out but isn't sensible, see 3
2) Change the product specification, for example, remove a feature you cannot implement,
3) The company goes under due to impossibility to deliver. You resign, or get fired. Yes, incompetent middle management or micromanagement, or insisting to arbitrary rules, can
really kill a corporation. A small company, even more easily.
Or, hopefully:
4) Everyone's sensible, and the insane rule stops being in existence. Everyone laughs at their stupidity together, and life goes on.
There's a yucky middle-ground, however, where everything kind-of works, never leading to a full-blown crisis, but such arbitrary rule becomes a productivity issue, causing timelines to strech and people to get stressed.
Depending on the viewpoint, all this is either called a "style guide", or "micromanaging". In any case, it's alarming to see such a corporate style guide in a company of two (IMHO).