Thats a bad situation! You want to have your cake and eat it too! I'm surprised that it has that 'feature'.. It doesn't sound like its very helpful. I don't know of any situation where I would be glad that it disables the lineout when the remote is plugged in.
While its always superior to plug straight into a line out, you can go from the headphone out to the TA, and still get better sound than straight from the headphone out to the headphones. Some people say its not worth it, but I think there is still an improvement. You are taking the 'weight' off the built in player. It doesn't have to actually DRIVE a headphone, just pass its signal along, so it doesn't ever reach the limits of its operational abilities, which is where the worst distortion occurs. Plus, you still get the crossfeed.
I'd say try it out the headphone jack, and then listen through the line out again, and go back and forth a few times. If you don't think you can live with the headphone jack, then look around for another player that doesn't have that 'feature' (or possibly find a way to disable that feature in the software? I know things like that are possible in some players, i have no idea about yours though). But if you think you can deal with the headphone jack, then go for it. Good portable sound is about the sound, of course, but the PORTABLE part of it includes convienience. The whole act of carrying music around with you forces you to make compromises for convenience's sake. If the compromise still results in acceptable sound quality, but improves your useability, then its AOK.
Peace,
phidauex