I only have Swap Magic 3.6; so, i'm sorry, i can't test it.
This only works on Service Mode.. on normal mode, the PS3 says that PS2 discs are not suported, or something like that.
On service mode, i don't see any protection about PS2 games, funny, but hey, better for everyone in the scene, i believe.
At least for me it was awesome to test it.
As i've said, you dont need swap magic, ou any boot disc like that.
Just put an original game, if you have the ps3 opened, and drive also, swap an original game, for a backp of any game, and you can enter and leave to the xmb, and swap for another backup, without having to start the method again.