How does FAF/vanilla SC:FA technically work?

Hi there,
We are a group of friends used to play SC:FA for years with our personal mods.
Now I installed FAF, played online once.
Seems I can still play our personal mods configuration by starting SC:FA standalone (which is awesome). Or am I mistaken?
How is it technically done?
Does the FAF client copy files back and forth to the SCFA bin dir?
Does it come with its own game binaries?

The FAF environment is largely separate from the Steam environment. We have our own binary folder with our own executable in it. And we have our own content folder that the vault populates with mods and maps. It was setup this way to prevent conflicting configurations with either your own mods (like in your case), or with LOUD. There's no further copying involved

As a note the content folder is only different if you set it in the options. Otherwise the default maps and mods folders are used so will be shared