I'm trying to map with the enhanced version and in order to do that I need to locate the "rerelease" and "fgd" folders to get files, but it doesn't appear to be in Quake 2's main directory, neither do the files. Would they be located elsewhere? The Steam version has them in its main directory, why not GOG's...

Quake Enhanced on GOG is installed separately in its own folder unlike the Steam version, whether its through the offline installer or GOG Galaxy. This is also applies to DOOM I Enhanced, DOOM II Enhanced, and presumably Quake II Enhanced (I sadly don't have this one yet).

Although GOG Galaxy and GOG builds a bit or very differ, you can use GOGDB site provided Galaxy builds filelists as reference.
(for many yeas gogdb show incorrect size it is bug of this website)