RM allows indies who actually RP in fighters. The last time good indie capship roleplay came in an RM box was.... never, so that's a bit frowned on, but if you fly RM colors, know what you're doing, and act like a member of the Kriegsmarine, we'll group with you and treat you like one of us. In RP, you are one of us anyway, faction tag or not. So long as you act like it there are no issues. Such people are so rare in numbers, unfortunately, that we'll almost certainly encourage you to apply and likely applaud you constantly.
All other factions are pretty much the same, if you RP as part of the group then you are part of the group. Gets touchier in bigger ships, for example, Rheinland's Navy has a whopping total of 14 battleships if I recall correctly. You can't exactly just make one like you can fighters, the names are all well known, documented, etc... and they aren't handed out on a whim.
Good indies bring more warmth to most people's hearts than good faction tagged players- supply and demand kind of thing. Go for it.
That said, the factions have a wealth of information they know where to find- its a good idea to talk to them for background you should be familiar with.