Okay, here's what you can do:
Install the autoupdater to the DEFAULT UI folder and run it from there.
Only place CUSTOM eq2map files in your customUI/eq2map folder.
The map window will check your custom folder first, and go to the default folder for anything it doesn't find there.
The autoupdater won't even be aware of the custom folder, so your custom files won't be altered, just like the game's own patcher.
The downside is the same: If any updates are added, you'll have to either get by without them or re-edit the file, just like we modders have to do when SOE updates the UI.
Added downside: The patcher will re-download the default eq2ui_mainhud_map.xml when you patch, but that doesn't really matter; the eq2map subfolder will remain intact.
If it ain't broke, it needs more features!