In the store page for Quake Enhanced, it shows Manual under Goodies. If I look under Downloads, there is no Manual to download. Only a single backup installer (Quake Enhanced 1.0 579 MB). I installed the game and did not see a manual in the installation directory either. Is there no manual that is included with Quake Enhanced?

No manual, yep.
There is old legacy html documentation for game and addons in game folder after installation for base old Quake version only (and only on GOG, Steam version now lack it), as well as pdf file in Goodies section. This one df for base Quake The Offering is listed on the store. You can download it without legacy base Quake 1 under Quake entire in your Library (not Enhanced).