With it set to final fire, would it still protect the whole planet? What about possible ships in orbit?
Yes, final fire protects everything in range, but only fires just before the impact. The only exception is CIWS with its "final fire (self only)", which works like final fire except, well its only for the ship itself.
By the way it can be somewhat better to build Orbital gauss-gun stations. They usually fare much better per cost in intercepting missiles, but on the other hand also require maintenance.
Yes that would all work.
The Fire controls with different ranges: What I had in mind is that it'd be able to start firing with decent accuracy at enemies further away, but having only long ranged fire controls would end far too costly.
Well I would say having one is ok, to gain some intermediate anti-ship capacity. Against missiles its nor really efficient though. At any way, you could easily reduce the other two in range by 50%.