Permissions errors typically come up when needing Admin access. Before attempting the desired procedure, open Blender by Right-Clicking the blender.exe and "Run as Administrator" (for Windows Operating Systems). Make the necessary changes (for example importing the fa_hotkeys.py), then you're all set.

When opening a file not created in Maya Config Lite, during the "Open" dialog box (file browser), expand the right side panel (or hit N to expand it), and make sure "Load UI" is unchecked.

Yes (but with caveats!) Maya Config Lite with other addons: MCL should be installed first, as a base, before any other addons are installed. If you already have a Blender version with other addons installed, installing Maya Config Lite on top of them will ruin (delete) your addons. Instead, you can either reinstall Blender (deleting any pre-existing addons if desired) and install Maya Config Lite fresh and then add addons on top, or you can use a Blender Build off the Builds website and have multiple Blenders on your computer so as to avoid any interreference with pre-existing addons. (it is recommended to install Blender Builds to a folder on your Desktop or Documents (not to the C: drive), and it's recommended to NOT use an Alpha build): https://builder.blender.org/download/daily/