When you say the "exact same flights", is that with the exact same flight numbers?

In theory, if you're booking different flight numbers, then there can be differences that have to be taken into account because of that, even though the operating aircraft will be the same. For example, you could find that booking airline A's flight numbers means that you will earn frequent flyer miles whereas booking airline B's flight numbers means that you will earn nothing. And that could in theory happen even if airline B's flight numbers turn out to be more expensive.

Also, sometimes people find that they have more hassle if they book airline A's flight number on a flight operated by airline B than if they book airline B's own flight number. Airlines have generally worked quite hard to reduce these issues, but they do sometimes still occur.

So the question of exactly what you'd be booking through each of these routes would be important.