It's been a while since I visited this thread... Only 689 posts? COME ON
Maxwell, I think you mixed up TV trasmitted/ TV safe with academy aperture. A double-system show that doesn't deliver to film has no reason to use an academy aperture. Also, Super35, 3perf etc. pertain to widescreen shows and were not prevalent at the time ST:TNG was shot. Panavision has a long history of supplying cameras for 4:3 TV shows and it would be untypical oversight to use the wrong gate or ground glass.
So how was TNG originally shot? Truth is, there's a myriad of frame formats for film, and some of them (like Super35) aren't even industry standards and have slight differences between camera vendors. It's also worth noting that Paramount had its own version of Super35 with a common top instead of centered. (see this Panavision document of current common GG formats.) The gate determines the exposed image area, and the ground glass guides the DP in composing the shot. This is why on film shows we shoot a framing chart, where we basically trace the ground glass. It's the only exact way for post-production to know the DP's intent.
(More information from IATSE 600, Hollywood's cinematographers union, on film framing.)
Also keep in mind that things might have changed between seasons and DP's. Full frame, academy, TV safe, hard matte, soft matte, who knows. Maybe inconsistencies were the reason CBS stuck to the common known clean frame of 4:3.
I was (over)thinking all this until I realized I have a bit of actual film from TNG. Here's a rough scan:
Thanks to Curt McAloney from StarTrekHistory.com, who pointed out Paramount released some film clips of TNG dupes. Look for them on eBay.
From this film clip it's obvious they used 4-perf full aperture, as expected. Now I have no idea which episode this is from (the package only says "On the Bridge of the USS Enterprise-D), but if you could find it in video it could give a decent reference of what was shot and what was delivered.
PS: for all the 'beta' references: ST:TNG was never mastered on Betacam (and predated DigiBeta). It was mastered on 1" Type C and later on D-1.