The last paragraph in your answer explains a lot, if not all. But then it also shows that, depending on the board house you choose, you have to take into account what they expect: finished or unfinished hole sizes.
This also means that, when you create footprints, you have to take into account the “worst case scenario”. However, while designing the footprints, you might not have any clue yet to which board house you will send your board. Hence, again the “risk” of choosing the wrong drill diameter while creating the footprint(s) for a new component…
And that is what puzzles me a bit: what’s the best approach here. Again, until now, I have no experience with board houses, I will step into the “realm of board houses” for the first time and I don’t want to shoot myself in the foot with those kind of things…