Yes. In fact a lot.

FWIW the only real + is one you didn’t mention, which is that IB is the most punctual airline in Europe. BA is not.

In any case the BA check-in desks at Madrid are staffed by IB staff, the same ones who at different times of day also work the IB desks. So they’ll know and do the same things. And in any case both sets of airline staff will look in exactly the same Timatic system before offloading a passenger for document reasons.

Pick the best timed flight for your itinerary and be done with it.