Ive used it before. Not with waterlox. But i dont think there would be an issue.
Ive found the finest dust along with small batches works best. The stuff sets up pretty fast so you need to work fast.

here's a picture of the floor section that used to be covered by tar paper, linoleum, masonite, vinyl, vinyl, ceramic tile.

Is it typical to do the filling after the final sanding or sometime after the second pass? Does Glitsa need to be drum sanded or will a screen on a buffer be better?

Thanks

You should get the floor sanded clean. But not the final sand. Fine grit sawdust is ideal.

The cement harden strongly. I suggest a drum sander. Or some means of agressive. The screen alone wont cut it.

Glitsa Wood Flour Cement is a good choice to use as a filler. It does need to be sanded off with the sander as a screen is not aggressive enough. I'm not a fan of Waterlox but it should be just fine to use over the filler once it is dry.