Yes, of course this is done intentionally, to prevent user to set wrong compatibility options which are not default and would conflict with our software. The only option that is left untouched is the "Run As Administrator", that is left as it is but, everything else is set back to default after running the FSDT Live Update.
Since we don't release updates every day, if you *really* need that option ( and it would be helpful to know why ) to say enabled, just enabled it after doing a Live Update and, only do a Live Update after you get a notification of a new one.