Bases/AOC's/IA's
Don't confuse AOC's and employing entities. One has no relevance to the other in the context of your question.
If you're employed by Qlink and based at either Brisbane or Cairns you'll be employed by Sunstate Airlines. The Sunstate EBA applies to you and you'll be placed on the Sunstate Seniority list.
If you're based at either Sydney, Melbourne, Mildura or Perth you'll be employed by Eastern Airlines. The Eastern EBA applies to you and you'll be placed on the Eastern Seniority list.
Pilots transferring to bases 'belonging' to the other company is relatively common. The consequence for the pilot involved is that they'll be placed at the bottom of the new seniority list as they're considered to be "new" employees of that company. Entitlements such as staff travel, long service leave accrual, etc, are kept as they're transportable within the group.
Upgrades/downgrades/fleet transfers may or may not happen; generally only if requested by the pilot (e.g. a Sunstate Q400 FO successfully transferred to Eastern as a Classic FO and a few Sunstate FO's transferred to Eastern to be Captains).
Having said that, it is a simpler process to transfer between Eastern bases than to cross companies. The previous resource manager created a "few issues" in a number of previous cross-company transfers but he's since been replaced. Time will tell how it goes in the future.
Difference in waiting time? How long is a piece of string?
In answer to your question, My advice is not to second-guess and request your base in order of where you want to be based. Be prepared for none of your requests to be honoured and to be based in the most inconvenient (for you) location.
DIVOSH!