Generally, I'm pretty sure it's fine to do that. Think of it this way. Lots of BakaBT members use seedboxes. The chances of two members using the same seedbox server just by pure chance is not super high, but still reasonable. Staff members don't have the time to hunt down everyone who happens to use the same seedbox.
Just don't seed a torrent anywhere else while you are seeding it on the seedbox. Your friend should be able to seed the same torrent as you are without a problem, as long as he's seeding with his account and not yours.
Of course, it doesn't hurt to make sure, so I'd go through with the IRC discussion regardless.
