I'd love to know the answer to this too as it seems like everyone adds the priming sugar solution to the bottling bucket before transferring, but as you mention, how do you know how much you will transfer over after leaving the trub in the bottom?
What I've been doing is what you said. Transfer to bottling bucket (with measurements on the side), then weigh out priming sugar based on that volume. Boil priming sugar and water mixture and then add to bottling bucket and gently stir.
BUT, I've had carbonation issues, so maybe it's better to use an approximation for the volume measurement and get better mixing by transferring on top of the priming sugar than it is to possibly get incomplete mixing by putting the priming sugar on top and mixing??