One of the most beneficial aspects of a military base and military ATC is the lack of 'positive' control. This allows flexibility in training which cannot be replicated in civil controlled zones. I've worked in both and it is quite a difference.
The notion of Gin Gin having a second runway is all well and good, but what time frame are we looking at here? Would probably end up being another Badgery's Creek. Pearce does have one parallel runway however I doubt RPT would enjoy the procedures in place for its use!
It may surprise some but within the military it is very rarely the case that facilities are installed on the basis of where the 'brass' want to live. (Why is that difficult to imagine?) As far as the Perth northern suburbs go are we talking Mt Hawthorn or Alkimos? When Pearce was built no doubt it was waaaaaay out in the sticks at the time.
The cost of working out of Learmonth is not just the move there. The ongoing fixed costs would be quite high, remote localities usually are, logistics far more difficult however great fishing and diving.
I don't understand why the Defence Dept is so precious about Pearce? If Darwin can be a combined civilian/military airport, why not Pearce??
A little research on how these bases work and you will have answered your own questions. Its not a question of being precious, its a question of protecting what you have. More traffic, more constraints, less flexibility (which is the key to airpower). I don't think anyone was particularly enamoured by the decision to allow the RSAF to train there back in the 90s. I can see the advantages for them but for the RAAF?