The original episodes were all recorded in wide aspect ratio, even though they were destined for broadcast TV. They were touted as future compatibility. So the original broadcasts were "pan & scan". Then, when the wide-aspect disc formats arrived, it turned out that converting them was not a simple matter of going back to the originals and plopping them on disc.
DS9 and Voy have the same issue. For DS9, Season 1 was shot wide screen compatible then they switched to 16:9 but none of the effects are widescreen ready.
Only the live action shots were recorded with a wide aspect ratio, and perhaps not even that for the pilot. The CGI was rendered in 4:3 and the final cuts including transitions and VFX where composited in 4:3.
The remaster combines cropped 4:3 but high resolution scans of the original live action footage with (sometimes badly) upscaled versions of CGI and VFX'd shots -- except for the pilot which is fully upscaled and cropped from the original 4:3 broadcast masters with zero high resolution live action footage. I don't know if the pilot footage was actually shot widescreen but if it was then you don't get any of it in the "widescreen" pilot included in the remastered versions.