The way I played out any ships that I had that were yellow on the master ship list was:
I made a character called "bribe" and transfered them an imaginary bribe, then deleted the character. I put that RP in the forums along with a story illustrating just how shady a non 'everybody is full green' deal is involving gunboats. The bigger the item the more nonstandard the event should be IMHO.
And I would say its never ok to cross the master ship list, no matter how good the RP is (and man some of it goes very deep and is top notch). Its OK to cross factions weapons and machinery IF you arent in one of the factions.
Now as far as that is concerned, I would also expect to be harassed by any actual players in a faction if I was using enemy weaponry in their territory, but usually only if its the whole loadout. I dont expect the outcasts to flip over one del cid, but they might get pissed if you have 6 skyblasts and a skyblast turret on a sabre.