I was wondering about LaLaLand, since I assume that's where they got the tracks from. LaLa would likely have a license or permission to produce CDs and would have copyrights over their form and presentation order, i.e., their specific reissue format, not the tracks themselves.
That is, you couldn't burn a bunch of copies and sell those, since that was LaLa's work. (Then on top of that, you'd be infringing the rights holder of the individual tracks, which I assume is CBS.)
In the case of Phase II, you'll see that we've had access to and have used the TOS music in all our episodes for almost ten years now--including tracks that have previously been unavailable before the LaLaLand release late last year. Although our source predates their easy availability now, I'm not sure what copyright implications might be now.