Correct usage of VDP ports following the standard

Lol @ ARTRAG

yeah bios you can forget in a game. except in a little game.
there is this idea "code it like a PC" and it is unclear what it is about.
if you think to code it like MS GDI X Window - even on pentium was not coded like that.

your only chance is to first code a game lib to the metal.
afterwards could come a library coding feel.

for MSX sprites I suggest the array of pointers to struct { Y X P C }
then comes the library call that brings it all onscreen with colorcopy fix and SAT dump.
then "PC" coding dream could reach top speeds
especialy when you make bubble free lists for bounding box collision checks, too.
all that stuff is on C struct level except that one SAT dump function.
and its implementation to the metal is not in conflict with neos, can be coded to variable port.

Official way for me (patching the code in RAM with the ports value read from BIOS for speed sake)!

there is also another thing that stop the use of the BIOS when doing time critical operations: the fact that the bios implements functions that are 'trusted' to do a task (I/O, set graphic mode, set a point, draw a line, set psg etc) does not mean that the BIOS IS THE SAME on every machine, implementation could vary.
plus the interrupt handler of the BIOS is 'sensitive' to hw configuration (floppy drive or hw that do interrupts).
the BIOS is fundamentally not only slow, but also timing-unreliable.

say we need to write a charater on screen at a specific time: the BIOS guarantees that the charater will be printed but say nothing about the time it spend to achieve the result. If you talk to bare metal directly you can have a control even on this aspect, (or more precisely you can have better control on timing).

I don't think there is a definitive answer. As someone said above, the important thing is to know what you are doing and be aware of the tradeoffs. If you really need to speed, and are ok with not targeting 100% of the machines, then direct port access is the right thing to do, otherwise, using BIOS should be preferable. But again, I think that that should be a choice of the developer, and what is important is that when we make that decision, we do so knowing exactly what using the ports directly or using the BIOS might imply for compatibility and for speed.