Ceoran, I think the BPA is also aware of the agreement - as long as you don't get caught smuggling anyway. Admittedly, I'm just guessing from that time a BPA pilot tried giving me orders that did not involve fines, removal from Bretonian space, or other such "omg pirate" matters...
Additionally, though I'm not certain if you'd know in-character, there is a trade agreement between Bowex and the Council of Dons. Take a look.
I'm guessing, if nothing else, that you'd have been told to let Bowex pass, if maybe you weren't told why.