It's a legit solo release...even if some people wish
they could get it for free by having it in the already awesome season 3 set.
Given what these sets are retailing for, it would hardly be free.
Hopefully the rest of the special features, besides the commentary, will end up on the season four set.
I do think it's a shame the commentary can't be included. Paramount had no problem editing Nick Meyer's commentary recorded for the extended version of TWOK to fit the theatrical version, for example. Unless the re-edited version of the episode constitutes a major departure from the original two-parter, they could do the same here. (Of course, it's possible the new edit is quite a bit different; it's also possible the commentary directly addresses the new edit, and wouldn't be applicable to the new version.)
Happy to hear they're not producing a 16:9 version, though. The season one features illustrated why that would look awful pretty well.