I'm talking about this:

https://github.com/X2CommunityCore/xcom2-launcher

On GitHub, it makes managing mods and starting up the game so much easier and faster. Currently it requires Steam and an online connection to it. Anybody know if there're plans for this to be updated for the GOG version of XCOM 2?

I checked the github page and someone opened an issue to see if support for non-steam installations gets added.
Time will tell if it does.

Let's hope!

Is there any way to manage mods at all other than physically moving them out of the Mod directory currently?

The Nexus Mod Manager works.

I'll give that a look, then.

Again resurrecting an old thread.
The alternative mod launcher (AML) can work with Gog if you do this described in the AML's github:
github.com/X2CommunityCore/xcom2-launcher/wiki/FAQ
Basically replace the steam_api64.dll file within the AML with the one in the emulator.

The download link for the steam emulator provided in the github explanation is not working, so grab it from the official release page here:

mr_goldberg.gitlab.io/goldberg_emulator/

I don't use this to launch the game as is unnecessary if you are already using the vortex launcher, but it can work for checking possible incompatibility issues if you are starting in a new campaign.

I do not use a mod manager.
Add mods manually is simple to do,
And for me more tools = more reason to have problems.
(but uses few mods : 20 or 25)

Thanks for this link, all mods now working well with AML (327 so far)

The game's launcher is outright bad, when using many mods it is simply not an option. The Alternative mod launcher lets you check for overrides and both the vortex manager and AML lets you install any mod fairly easily. You certainly are not forced to use any of them, but if you want to save you from headaches it is best to use another launcher.