Yes... And i'm really sad if is it true. Like the OP wrote, I also was glad about to still be able to customize our looks and stay viable in end-game. But with these bonus sets: this statement:
"...we also made sure of dropping purple Armoring mods of equivalent power as Operation loot. This means that players going the mod route can still take their favorite orange armor and make it as good as a operation purple armor (with some temporary caveats)."
From here http://www.swtor.com/blog/some-clarifications-item-modifications
Seems null...
Otherwise the OP gave a good idea if not implemented ingame yet:
or is there a special mod which is buy-able (obviously not on the fleet since I've looked multiple times) with Operation commendations which grants the set bonuses to a piece of custom loot
I complete this idea with: if a set bonus gear piece can be exchanged using comendations (PvP, etc.), THIS special mod item with the bonus could be exchanged using exactly the same comendations. What would be just an option for the player: to buy the gear piece or to buy the special item, in both cases the bonus would come! And if we have set bonus pieces dropping from bosses, etc... THIS special mod item should drop as well!