Current prices of S3 Trio64 and its great DOS compatibility make it a great pick to have even if you're not going to build around it.
This card was always universal choice, like Trident TVGA9000 for ISA systems.
And it is actually an 2D accelerator, so regardless of DOS games not using it, it is great to have it on Windows on a 486/P54C to have smooth SVGA experience.
But there is another thing,
In my DOS PC which is pizzabox with only 3 slots, I dedicated one to a Stingray Pro card, while having Trident TGUI on board. Both have same 1MB, both are highly compliant for DOS games, Stingray is faster because it's one of the fastest PCI cards around, but Trident has Windows acceleration. So why did I decide to waste a slot?
Picture quality. There are many factors involving picture quality but this onboard solution sucks compared to Hercules. When talking cards that have bad output there may be some ailments to be applied, but onboard very much unlikely.