The Devs seem pretty clear but to spell it out:
BM, Champ, Cent, Tion, Colu, and Rakata mods and armoring WILL NOT have the set bonus on them. They are on the shell only. If you remove an armoring it will not have the bonus. It doesnt matter if u buy them pre or post 1.2. You cannot transfer the set bonus with these pieces.
Only the new tier of gear, War Hero and 1.2 PvE will be able to transfer set bonuses.
This gives us a choice, is the set bonus really worth 5 Augment slots on crit Orange gear. My guess? No