IIRC, bonus for shipbuilding is only for the planet that builds the ship (same with troops BTW).
The treaty thing you suggest may work, but you will need a willing partner as the other empire has to confirm the NA
The penalty (10) for colonizing is empirewide and is for every planet you colonize during the whole game. That is the hard part.
-50 for capturing a planet are good. When you have your troops ready, start raiding and your people will be jubilant in no time