While the physics loop frequency may be 100 Hz (or any other value; it's not important) it's always possible to interpolate between the positions that straddle any given checkpoint and thus produce a timestamp with higher precision.
(Edit: perhaps I should add that there's nothing at all fake about this. It's actually *less* fake than using the timestamp of the first position update which is beyond the checkpoint. That may not be what LFS does of course - I don't know.)