Just connect it with the optical s/p dif input of your md, with the right cable... If your minidisc doesn't have optical input, you can't do it... Unless you buy a convertor from optical s/p dif to whatever input your MD does have...
Hmmm.... is the ATRAC algorithm built-into the converters? If so, then by using them you are applying the ATRAC and losing a good chunk of your signal.............
I dont think so because you can do it without recording anything to disc ,and if you did, it does sound different, somewhat cleaner like if you used noise reduction.