You will need to add a Deployment Share to MakePE if you are going to want your Bootstrap.ini or LocationServer.xml.
If you are using your Deployment Server with MakePE, then just specify the path in the MakePE\ScriptsRW\MySettings.cmd and you are good to go (I have not tested with spaces in the path).
You can even specify a UNC Path (I have not tested with spaces in the path) to a Deployment Share.
Additionally, I use MakePE on a clean OS on a Virtual Machine that is not joined to the Domain. This keeps my MakePE Environment clean (from Policy and Agents). To keep the MDT step from throwing an error, I simply add a Net Use command in one of my Build Scripts and I will be prompted for credentials when I kick it off. No need to map a drive letter . . .