The Documents folder contains only "dynamic" files, created/downloaded independently of the simulator itself. These include scenery files, logs, tools, etc. If you have problems running applications from the tools subdirectory, you can safely copy them to any folder, but you must remember that after a new release of 'Scenery Packages' the tools are overwritten with the new necessary files, but these 'exe' files change very rarely, so I think this is not a problem.

The simulator itself installs to the directory you specify in the Launcher configuration.

In addition, it is possible that your antivirus software probably allows you to create exceptions to bypass problematic files/folders.