I think the "Black Isle" seeming-slam that most folks at BIS noticed was in a slice of dialogue in Arcanum referring to the "you mean the Black Isle?" and a follow-up of, "no one would ever want to go there," - I think it was in segments related to the Isle of Despair. Whether it actually was a Black Isle slam, I don't recall, but it was easy to interpret it as one. I don't think anyone really gives a shit about it all now, though - I don't.
But that said - the tension within the studio was pretty unpleasant following the departure, and it was mixed with a measure of confusion because it wasn't clear at first what had happened (or why it had happened), just that everyone leading FO2 was suddenly gone.
Considering what was going on (hey, Fallout's successful, why doesn't every non-developer in every part of the company jump in and try to guide the ship despite the fact it's going fine already), I don't blame anyone, that situation basically sucks - but I only saw it/heard it from the outside, so take that with a grain of salt.
I will say FO2 suffered without the three of them heading the ship and maintaining the vision - not to mention the subsequent loss of other folks who jumped ship, even if they weren't working on FO2 - we lost a lot of good people. But hey, that says just as much about the studio unable to keep them on board as much as the promise of better opportunities elsewhere.
I still rue the fact the original F2 artwork for the game cover was never used. :/