Makes sense to me. Assets are controlled by a faction, but that doesn't mean exclusive use of them. %influence equates to the % of the population who support that faction. That population can't exist in the vacuum of space just because all the assets are controlled by a different faction.Well factions with no assets also are in blight. This does not make any sense.
That and factions clearly conduct operations aboard non-controlled assets, thus "industrial supply" missions and the like offered by non- controlling factions aboard.
Tl;dr the controlling faction is just the one collecting the rent on leased subfacilities.