You're almost right, cemole.
The 2 differences between the installed folder and the mycustom folder are that the aliases under installed are read-only, and can be changed with each update of farr.
So, if you move an alias from installed to mycustom, it won't be updated on farr update, and you'll be able to change stuff.
Also note that currently, the nircmd alias can't be updated throught the DCupdater, but the core aliases can be changed in a farr update.