For those who might like to know.

The Addons from the GOG version work out of the box, copied to the main Quake folder, even for the Epic and Steam versions, though with the Steam version you need to do the text file with the game ID in it, to avoid the Steam client starting up.

So if you have a path something like - D:\Games\Quake, you can copy an addon folder to that, like - D:\Games\Quake\Honey, and execute it using the following command-line in a desktop shortcut, with no need to bother with the EXECUTE button found in the Quake menu Addons entry.

(GOG) D:\Games\Quake\Quake_x64.exe -skipmovies -game honey +map start

(Steam) D:\Games\Quake\Quake_x64_steam.exe -skipmovies -game honey +map start

(Epic) D:\Games\Quake\Quake_x64_egs.exe -skipmovies -game honey +map start

So you don't need to stick to Addons being located in the Saved Games folder, where they originally download to.
C:\Users\Timboli\Saved Games\Nightdive Studios\Quake

I tested the Epic version with the Quake download I got via Legendary, which I had done on another PC, then compressed to a 7-Zip self extract executable, then extracted to a folder on my Wife's Windows 8.1 laptop.

As well as the addon 'honey', I also tested 'q64' and 'bbelief'.

P.S. Using the specific command-line I did get an error popup when trying with the Addons on my Win 7 32 Bit PC, so 64 Bit is required. If you want the music to play with the addon, just copy the 'music' folder to the addon folder.

i.e. D:\Games\Quake\q64\music

NOTE - This post was copied from the following thread, where more background information is available.

https://www.gog.com/forum/general/quake_enhanced_update/post379

-skipmovies is the key.

Alternatively, renaming D:\Games\Quake\movies to something else also works.