This is not yet in read me file, but, anyway, as i say before. there is design difference between Install and Portable versions.

Version with installer:
1) Can be installed anywhere. User not asked about installing it to game directory (like almost any other program)
2) Can work with any directory. MM will ask for a game directory on start if it's not defined
3) Can auto-update itself (i hope this will work )
4) Config is stored in AppData

Portable version:
1) Should be placed inside "Game Directory\Tools"
2) Can work only with "..\" directory
3) Cannot auto-update itself (but still can check)
4) Config stored in MM directory

So answer to your question "prefer to not do this". Reason is that MM is not limited to one folder, and can work with different directory. But if you insist...