Exactly! I got tired of seeing READ-ONLY and moved ALL the core aliases and icons to the MyCustom folder. Not being able to edit those seemed like having a web browser preloaded with 200 bookmarks that I couldn't modify, and I didn't want to work around it anymore.
The only thing you have to worry about is that the readonly built-in aliases are overwritten when the program updates. So just remember that if you replace the built-in aliases, make sure you dont rely on having to modify the built in alias files -- instead disable the files that you want to replace.
(or of course you can always use FARR portably and not overwrite the alias files).