I'm not much of a music editor, so I would never attempt a project like this for even a single episode. But I have formed a couple of impressions lately of tracked episodes.
"The Lights of Zetar" struck me as a really good one. The music from WNMHGB seems, if anything, even more appropriate in this episode than the one it was composed for. It comes off as perfectly spooky and atmospheric in moments when "Zetar" is going for that rare thing in STAR TREK, horror. It really clicks.
But I just caught "Let that be Your Last Battlefield" on TV and the tracked music seemed clunky in places. "Elaan" works well enough when Bele's invisible (read affordable) ship is coming at us, but there's a use of "The Empath" in sickbay at one point that stuck out. Overall the tracking was kind of patchy and disjointed.
Maybe the uncut episode on DVD is better, but surely not that much better. LTBYLB would have been elevated to Fair or perhaps even Okay status if it had been given it's own score. But as a tracked ep it never gets off the ground.
My favorite tracked score would have to be "This Side of Paradise."