Just a few additions and corrections...
Both 3D shorts were originally shown in a Polaroid presentation, not the red/blue anaglyph. What you're seeing on the video here is a conversion to that format. Seeing one of the shorts "flat" simply means that they transferred one "eye" (3D was projected with two strips of film, one with a left eye view, and one with a right eye view). SPOOKS! was originally sepia-toned, not for any aesthetic reason, but for a technical nature (as was MAN IN THE DARK, the film it went out with).
I don't know in which order the shorts were shot, but in release order, SPOOKS! is actually the first wide-screen Stooge short (as is everything onward from that point). For the remake shorts, much of the footage from older shorts that was incorporated were medium and long shots, which you can "get away" with when cropping them. When they had the opportunities (ie. when Shemp or Curly weren't in the shot), White seems to have shot new re-composed close-ups with Larry and Moe to compensate for the wide-screen cropping.
The widescreen presentations, in my opinion, are almost a necessity, particularly in later shorts where no care was given to things falling just outside of the 1.85 frame, such as boom mics, and edges of sets, etc. In SPOOKS! for example, the opening joke is totally ruined in an open matte transfer when in the full frame you can read the punch-line painted on the door before the camera pans down.
