I've toured both ways with the same tent on the same tour -- parallel and at right angles to the centreline of the bike.
I would, in general, opt for the parallel method. As Bezalel says, placing it at right angles interferes with opening and closing panniers, getting to stuff inside those panniers, and removing the panniers from the bike if you have to get on a train, for example (getting to the release mechanism on the panniers can be a chore, and then lifting off the pannier quickly is really problematic).
The only advantage to putting it at right angles is to put another bag on the rack, and that only makes access issues to the panniers worse.