There are definitely RP opportunities precluded by the ban on multiboxing, like what you've suggested there. If I'm understanding correctly, you have an idea to do around about the same thing like what Orillion did in SP, driving his Osiris around with a strike force inside it for use in operations deep in enemy territory, but even in that case the rules that exist preclude most factions, probably including the Order, from actually doing this (at least in house territory). Almost every rule made, from ID rules to server rules precludes some valid RP opportunities, but they all came about quite organically as a result of people taking the freedoms they had too far. Technerf rules so people don't just fly whatever ship with whatever guns they want because they can, ID restrictions to stop people based in the Edge Worlds rolling up to New York and camping it with 20 dreadnoughts, weapon class restrictions on caps because people used to mount tizzie turrets on them because they were legit a lot better than cap guns at the time.
The rule against multiboxing definitely does preclude some opportunities for cool RP, or place restrictions on people that make things unfun in certain situations (like said cap pilot not being able to join on one of his fighters while his cap sits out of harms way), but would removing the rule really do more harm than good?