Well, what he said in that quote is nothing I would call negative. I mean, he's Avellone and we assume that his ideas are good/great (and they probably are, considering his record), but I think it's only fair that a project director or lead designer has the final say on his game's vision, despite what the owner of the company thinks and ofc as long as that said director/lead designer doesn't fucked up with the budget or with the timetable.
Now, think if instead of MCA and Obsidian we were speaking of BIS and Torment or Fallout, and Fargo/other owners would impose their views on Tim Cain or Avellone himself instead of giving them the freedom to do what they though was right, the game would've been changed and not for the better, probably. On the other hand, the strange thing is that MCA didn't have a lead role on anything except Alpha Protocol (which was initially in the hands of other devs, though) and before that, KotOR II, that were released respectively 6 and 11 years ago. As an owner, he should've had the freedom and power to start his own project (and even Feargus said something about offering him the chance to go wild in their next KS which was supposed to take place around Q2 2014, then something changed apparently).
Maybe he himself didn't want to lead an Obsidian game, and he even said that in an interview, but I think that stance is referred just to his last years at the company in which he preferred to work on other stuff and accepted many other freelancing jobs.
