But wouldn't they spend most of their time shipping cargo between established worlds, and not so much on the frontier? Not much point in selling plasma phase converters to primitives that barely mastered indoor plumbing, is there?
The most lucrative market might be at the far frontier, really. Not only would there be primitives who'd pay good alcohol or pergium for electric razors and other trinkets - there would be the potential for meeting advanced civilizations that might accidentally sell something of great value in the regular market. Neither of these deals would benefit from the careful official oversight one would encounter deeper inside the UFP.
Transport vessels do operate in unexplored space, not just in the pathfinding days of ENT, but also in TOS: for some untold reason, the Antares
visited Thasus in "Charlie X"...
As for the one known indication of a civilian ban, the wording in "Inter Arma" remains a bit ambiguous:
Bashir: "I suppose it would be naive of me to point out that interfering in the internal affairs of a sovereign power is explicitly forbidden by the Federation charter."
Forbidden from whom? If the Charter establishes organizations within the UFP (like the Franz Joseph version, derived from the UN Charter), such as Starfleet or the Interstellar Court of Justice, it may also contain specific regulations on what Starfleet (or, in this case, Section 31) is banned from doing - regulations unrelated to what the Interstellar Court of Justice, or the UFP government at large, might be banned from doing.