I used to set my saddle height with reference to the ground (i.e. be able to touch the ground with both toes). Then I used the flat heel/foot at 90 deg to allow the knee to bend slightly in normal postion. So that's better and the saddle was then in proper relation to the pedal. I then ignored any issues with foot on ground at rest.
But then if the BB height goes up, the saddle must go up too. Even if this doesn't present a foot-on-the-ground issue, however, the saddle has now moved up and away from the bars. On my MTBs I think I have found a conflict between getting the saddle to pedal distance right (my legs felt cramped with the high BB) and stretch to the bars. I don't think I imagined it. It's OK if reach isn't an issue for you but I struggle with it (as I have mentioned many times).
I'm going to check it out again. If the BB height really does make a difference, it will be something to take into account more than I have in the past in deciding whether a bike frame is right for me or not (there's not much left not to have to take into account...
).