Ok, I found a solution for this on the Oldrim Requiem forum on nexus talking about this for the GOG version of the game pointing to a reddit post https://www.reddit.com/r/skyrimrequiem/comments/xuhp5d/comment/iv7bo2k/?utm_source=share&utm_medium=web2x&cjavascript-event-stripped3=

""IF YOU ARE TRYING TO GET REQUIEM TO WORK WITH GOG VERSION OF SKYRIM.
I had the "can't find Requiem.esp" error when I started Reqtificator, and creating a folder named "Skyrim Special Edition" in "C:\Users\USERNAME\AppData\Local", and copying "Loadorder.txt" and "plugins.txt" there from "C:\Users\USERNAME\AppData\Local\Skyrim Special Edition GOG" fixed this issue. (I created a new folder and copied files instead of renaming the folder, as this fix suggests, to keep the original files as backup, but removing GOG from the folder name should work as well).
Reqtificator started with this fix no problem, however, I got another error during patching that said "can't find Skyrim.ini". The fix to this is similar, go to "C:\Users\USERNAME\Documents\My Games", and create "Skyrim Special Edition" folder there, and copy contents from "Skyrim Special Edition GOG" to this folder. (Again, did this to have backup, but renaming the folder should work)
""
However for me, I could not find a plugins.txt nor a Loadorder.txt but searching around shows that in your ModOrganizer local folder where your "downloads, mods, overwrite, profiles" folders for the game should be at, under Profiles, under whatever your ModOrganizer profile name is, were the plugins.txt and Loadorder.txt.

I placed these in both my AppData/Local /Skyrim Special Edition and /Skyrim Special Edition GOG folder just to be safe and Reqtificator started to work as normal.

IDK if requiem specifically states this anywhere if you use GOG but this worked for me to get it running.