I believe satisfactory solution does exist. Like said it's to have a market of third-party engine manufacturers that is not exclusive to any faction. Then if you'd want alternative engine effect for your ship you'd buy one of those, if you'd want engine that belongs to another faction then probably would have to jump through a few hoops to get it inRP, and if you're content with first-party engine that came with the ship then you just continue to use it. May be have a few rare ones too.