With the right tube brush you can get the inside pretty clean. Besides, the outside fillet should give the joint most of it's strength.
It's true that a standard mitre will have its own challenges (keeping the two ends in phase, and all the tubes at the same length). You can creep your way into equal lengths, checking every second file stroke or so... You can always keep the shortest and adjust the others. It's possible you'll have to bin some tubes, but that might also happen while attempting to drill the through holes.