Thank you for the detailed reply and for the doslib test programs. I will look at the datasheet carefully since I was trying to understand by merely reading the code differences. Now I recall that there was a dosbox-x issue open with Corncob 3d, I think it must have been tested in VGA code running in EGA mode, and whether the timer code changes will address that issue or others.
Confirmed that the vmemdelay of around 1000 is sufficient. It's also possible to cause the same issue and solve it in pcem by modifying its isa timing function. The issue led me to debug some issues in a dos source port of doom, and if you are interested in testing it with your latest code base, I can upload it.