Many Factions like it when you have your transponder beacon on. Some factions don't care.(Well only the pirates)
As it stands, when you have a faction commission and you forget to turn your transponder on the faction you have a commission with will like you less as a result of that.
My Suggestion is that this does not happen when you have a faction commission unless you refuse to turn your transponder on when they ask. And they will stop following you as soon as they positively identify you. (so you can blip your transponder at them to say "yes, i am friendly"). This of course would be negated if they suspect you of smuggling.
The reason is simple, when you've got a commission you're working for them and your hiding, while not ideal maybe, isn't there to hurt them, its because you were doing something special and secret that required it. The equivalent of a plain clothes cop flashing their badge.
This would alleviate a lot of the "damnit forgot to turn my transponder on" complaints that people have while also providing and in-world rational for having that advantage