Spike -
Those are good observations and great ideas. I do know that the wastegates are done that way for clearance. When I had Tom do a motor for me before, I brought up some "new" ideas and he incorporated many of them in the build. He gave me good feedback on the ones that weren't such a hot idea.
If you don't mind, I would like to bring the throttle body one up.
Looks like you've been down this path before.
Thanks.