Are these going to be used in the official Freespace 2 SCP? And any chance of remastering with live instruments
Probably not. They're not really set up to be used as music in the game. They're continuous tracks with no spacing between phrases like there were for the originals. It wouldn't sound as good. He's also selling these tracks, so it would probably be in bad form to put these in-game, even if he is doing this because he likes the community and his old work. It would be the same as piracy.
Real instruments? Are you kidding? The answer is no in that regard as well, but this is probably the closest Dan can get to real instruments through a DAW.
I do wonder if a FreeSpace 2 remaster in the same vein is planned, though.