It is possible to rip 3D blurays to an mp4, mkv, and various other video file formats. You can also choose whether you want side-by-side, top/bottom and if it should be full- or half-width. Either way, it still falls under the same legality as backing up your movies, but that is beside the point.
My question mainly concerns putting any generic stereoscopic video file. Since Youtube basically works off side-by-side, I assume a side-by-side 3D file should work, but I don't know if it requires a specific format. You seemed to believe pretty strongly that you were unable to add 3D movies to the device, so I'm curious why you think that or if you read that somewhere.
As far as the OP, I agree with the others that you would still need red/blue glasses. If you instead were to rip a movie (that you own) that is in stereoscopic 3D, then I am pretty sure that you could place it on your device and watch it. I could be wrong, but I see no reason why you couldn't as long as it was encoded in the correct format.