I love Spooky as much as everyone here (HWN CE on order myself), but issues like this are partially of their own design.
Most people look at Stern and expect a pinball machine to spring to life fully formed with code and assets like Athena from the head of Zeus.
Spooky's model is more like watching a crew build a Frank Lloyd Wright building. Lots of WTFs and confusion, excitement and disappointment, until the final product takes shape and you can see what it actually is. So you have to be prepared to swing with the highs and the lows.
I never expected folks like Bowen or Scott (or even Eric) to be there full time. I always assumed they were "contracting" for the lifetime of a given game, since that's how Spooky does things, one game at a time. So he's not "contracted" for this game.
It's okay if they choose not to take his advice, as not every game needs to play like a tournament game say, and that's fine.
The only thing that concerns me is that Bowen says, "I no longer work with Spooky". Does that imply "bad blood" or something? That's my only real concern. If Spooky cannot retain proven talent over time (Scott, Bowen, Eric), then that's a real problem. I'm not suggesting they haven't, as folks might come back for contract games in the future. The thing is we just don't know.
So I don't think it's worth freaking out about just yet. Give it time and let's see what the building looks like when it's done.