The sense is that the commander of B5 is empowered to speak on
behalf of his government the way a captain exploring new places is
similarly empowered. One thing that Sinclair does *not* do is order the
Ambassadors around. That would be a significant breach of protocol. They
are all on equal footing in that respect. He is forbidden from using the
station personnel or firepower to, for instance, hammer someone into
signing a particular treaty, since that would be duress, and would be
considered void. It would also probably lead to a major confrontation that
nobody wants. There are definite checks and balances put in place on B5,
as with any other major installation like this.
Sinclair, btw, was not the first choice for this post; they wanted an
actual ambassador, but for reasons we'll reveal down the road, this didn't
happen. At one point we'll deal very straight-forwardly with this whole
civilian vs. military question in the series, which should answer many of
the questions being asked here.