The question of floating floors in bathrooms has come up before, but I'm not sure I've seen a definite answer. Here are my initial thoughts:
Seems like the weight of the toilet will pin the floor in place, in which case adding screws through the flooring under the toilet is not a problem, flooring wise. So the only question is whether the flooring is sufficiently stiff to properly support the flange; if it has a foam backing, it's too crushable to support the flange. In that case you could use an annulus of some more rigid material (suitable for use on concrete) to support the flange, and butt the flooring up to the flange.
Another question is whether anything else is going to pin the flooring in place, like a vanity cabinet on top of the flooring. It seems to me that it's fine to pin a floating floor in one place; then any expansion and contraction happens relative to that fixed location. So if one wall is 4' from the toilet, and another is 8' away, the observed expansion would be twice as large at the farther wall.
But you don't want to pin the flooring in two places. If you had a toilet pinning it one place, and a vanity cabinet pinning it in another place at some distance, I would certainly expect the flooring to buckle between the two if it ever had to expand.
Cheers, Wayne