If both have the same ideologies, willing to work together, don't see why not. But multi-billion/trillion companies are vastly bigger than a bunch of farmers and political enemies of the state.
If we have this parameter, then I think it could be possible. So in my opinion it's much easier to have a Bowex-Gateway merge sine they are both Bretonian shipping companies and their differences are quite small.
Unfortunately factions like Planetform and Synth Foods which are very "unique" in their activities and even though other factions produce large quantities of food (Samura) or are able to terraform planets (Kishiro - see Okinawa), I don't think they have the RP background to merge with a shipping or another company.