Hmm, interesting idea to give away some cash to the faction, who owns the base where you sell something. But I think that wouldn't be an improvement, rather then just indirect powergaming.
And I don't think that the powers of setting the prices would be abused. All of the official faction leaders can be considered trusted members, at least in my eyes. Otherwise they would not have been approved.
I was looking for some way to strengthen the ties between my ALG and our allies (Gateway, Kruger, IMG) for a long time now, but I couldn't come up with something better than some forum RP and bonus payments for the deliveries. If I would have had a possibility to set the prices of certain commodities for their IDs, that would have been awesome.