1. Would these cost fleet supply? Because if yes, it would be pretty wasted when your trade routes are well within your territory. What I think would be much better: A general patrol command in the fleet menu that could be issued like qued orders both within and between grav wells. For example in this part of a map:
M - N - M
|
E
My planet
Neutral uncolonizable grav well
Enemy planet
my trade ships going from M to M are vulnerable in N. So I set a patrol between both Ms, the ships jump back and forth until they encounter an enemy (in N) they will stop their patrol, attack, destroy (or maybe the enemy retreats) and then resume their route. 
A general escort command would also be cool, like the attack medium range command, just tied to another unit (e.g. order vasari flak frigates to follow and protect the mobile starbase.
2. No, with the last expansion turrets and hangars where allready upgraded so they can actually protect your civilian structures. That's pretty good as it is
As it will be possible to play only the 2nd addon without Entrenchment your idea would be useful in that case, just not in addition.
3. Yeah... Manipulating phase lanes sounds cool Maybe a tech like the super weapon (maybe even only one of multiple late game super-techs). I'm thinking of some abilities for civilian labs: far sight for all races (like the advent have as a cap ship ability), create new resource asteroids, remove/change/create phase lane... The last two would be restricted to the grav well the lab is in, so they get another purpose than just being build far away from the front worlds.
