Generally speaking, you need a filler that will not be attacked, or degraded, by the floor coating.
Epoxy will stand up to urethane coatings just fine.
I didn't fill any cracks in my floor before I coated it.
#1, I didn't fill the small cracks because my shop is a "working" shop with lots of welding, cutting, machining and heavy stuff being wheeled across the floor...some damage to the surface is inevitable. My shop is not a show piece.
#2 The few small cracks that are present were pretty much filled by the epoxy floor coating. You can still see them if you look closely but I have a lot of equipment that covers a large percentage of the floor and they are pretty much covered.