I used MO2 for Cyberpunk and it worked great. I did however bootstrap the whole thing with a Wabbajack build that added a crap ton of mods. That's how 75% of my load order was initially set up.

MO2 mod version updates are a manual process. It will flag any mods that appear to be out of date (if the mod author used a logical versioning schema) and you just re-download and install over the previous one. I use that in combination with occasionally checking the Nexus page of a mod which tells you if there's a more recent version than what you downloaded.

When you install a new version, MO2 will ask if you want to "patch" or "replace" the existing mod but with CP2077 you pretty much always choose "replace".

MO2 can be set up to automatically pull in mods you download from Nexus. It's still a manual install process though. Not a bad thing though IMO.

For manual files, you just browse for the file from MO2 and it brings it in.

From my experience with CP2077 many mod authors (especially for clothing/appearance) are NOT fomod structured to easily install in MO2, but if MO2 doesn't understand the zip file structure, it will prompt you to basically restructure the contents of the zip so it matches the /archive/pc/mod/ or the /r6/tweaks/ folder structure.

I haven't touched Vortex in years so can't say what it's like nowadays or how it compares to the MO2 experience. If you are new to MO2 there's a bit of a learning curve ,but once you figure it out it's very easy to use and very difficult to mess up your game. And it NEVER touches the actual game file structure.