im somewhat confused by what your saying, do you mean to say that an AIFF/whatever file being played on an iPod will sound better once put through a stereo/reciever/etc as opposed to headphones?
What I am saying is that there are two ways to get the sound signal from an iPod:
1) Through the headphone jack.
2) Through the line out from the dock connector.
The signal that comes out of 1) is already processed/amplified by the iPod internal components. It has been discussed in other threads that the quality of this signal varies from model to model and is usually worse in iPods compared to Sony Walkman, Zune HD, etc., because of the cheap components at the end of the chain that Apple puts in.
As you mentioned, playing lossless files in the iPod through the headphone jack will not really be any better than playing the same file in the computer. It does not matter if you connect the headphone jack to the car stereo, home stereo or high-end headphones. In this case you are bound to the capabilities of the iPod to produce good sound.
The signal that comes out of 2) in unprocessed. If should be similar in all iPod models and is basically the reconstructed signal from the losslessly compressed file.
If you put that signal through the car stereo, home stereo or headphone amplifier, you should get better quality as the processing is done by a higher-end equipment and not the iPod. In this case you are bound to the capabilities of the car stereo, home stereo or headphones amplifier.
Playing lossless files in the iPod through the line out will be similar to, better than, or worse than playing the same file in the computer depending on the quality of the equipment compared to the computer.
I hope this makes sense.