Doesn't the manager say in his profile if he takes control of stuff? I thought it was in there. If not, yeah, we should likely be more upfront about what he'd let you do.
As for the above case, I'm a bit surprised at the lineup that's getting suggested. If it were my game, I'd be opening it up in the debugger to figure out why the manager was doing that. I can tell you that if I'd seen a lineup case like that while testing, I would likely have gone in and done something to fix that