Yep, there's absolutely nothing wrong with just copying the entire folder anywhere you like.
We actually specifically store the saves and other user data in this folder so that it's super simple to:
1. Copy the folders anywhere like this.
2. Have as many installs on one machine as you want (say, with different versions, which some people do).
3. Zip up the entire thing and move it to another machine without hunting in many locations.
Etc. I know the SOP that is recommended by the OS, and generally I'm in agreement with that. But here we felt like the advantages of the way we do it are really strong. A lot of indie games do this for similar reasons (Minecraft comes immediately to mind), although we all kind of did it at the same time rather than seeing one another doing it.
Cheers!