I've checked on Amazon and clicked on all the links posted. I cannot find the 1999 Two Episode per disc DVD's for sale anywhere. None of the DVD's listed have the full 52 minute running time per episode, although one of them said 51 minutes. However, that's still one minute of footage I don't want to miss!
Star Trek on DVD never ran 52 minutes. If episodes reached that length without commercials, they would have had the one minute previews attached and with the "sponsored by" and "station identification" billboards attached. Without the previews, the episodes run, uncut, about 50-51 minutes (The Menagerie part 1 ran 49 minutes to make room for the expanded previews). Nothing from the 2 episode DVDs are missing from box set. No footage from the DVDs are missing from the Blu-Rays. The previews are not attached to the episodes, so that's a minute each right there (a minute 30 for The Menagerie).
Aside from The Tholian Web issue in the first release, and one or two glitches on the VHS tapes, the episodes on DVD have the same content as the VHS and Laserdiscs (trust me, I still have every episode from each format released except Beta). No scenes are missing. The only alterations these days concern the sound mix. Otherwise, no matter which format you choose, you are not going to miss any footage (again, except for the Tolian Web stuff in the first DVD release).