Have them need to be bought, stolen or killed for, basically never dropped in combat (max level salvage only, if ever? Plus requiring (and costing) way more industrial equipment than is generally feasible to recover), and have it hav limited charge of how many relation points it can eat before the observers check your signal thoroughly enough to see through the rouse with the difference between your actions and the relationship between your victim and the flag you're flying multiplying the charge drain.
It'd tie in well with the accumulated relation hit you get currently with running transponder off and would function well either as a pointsink for relation hits or as an impromptu stealth system.
Also, the relation hit you've banked on a false transponder should be, if you escape eyes before you turn it off, rolled up into a number, multiplied by a factor based on the difference between the ending balance of your false flag's relation hit banked (starting from neutral) and the actual relationship between the target and the faction you pretended to be and then multiplied by the military strength of the two party's local markets and that number is used to determine how much fleet points get spent assembling and dispatching a joint series of hunter-seeker fleets that attempt to hunt you down and figure out who you were.
That way if you pretend to be someone that hated a faction and bombed their station out of existence, neither side would care or believe it when the report that that ship that did exactly what we expected the Pathers to do wasn't actually a Panther, and if you're hated by Sindria and use a false flag to safely run an atlas full of food to a famine-stricken Sindrian world for profit, once they realize you weren't the ally you pretended you were, everyone involved shrugs their shoulders, burns the report and moves on with their lives.
But if you pretend to be an ally to make a strike or pretend to be an enemy to make profit off of making peace terms, the two parties are hurt not just by your actions but by you undercutting their legitimacy, and governments HATE when you do that