jOc: welcome to the site, and thanks for the kind words about FARR. You've probably gathered by now that the software on our site is heavily driven by user comments here on the forum, so keep the suggestions coming -- we take them extremely seriously.
as jgpaiva points out, it's very important that you solve this by disabling the built in aliases (and then doing what you said you did, copying the ones you like to your personal alias file/folder).
why?the reason these alias files are marked as read-only and make it so hard for you to modify them is because they are replaces when the program is updated. this approach was actually a lot of work, but i implemented it specifically so that we could allow users to easily modify their own aliases, and share aliases, while still making it possible to update aliases (both included with farr and shared by others), without risking erasing the users aliases. so that's why that checkbox is there, so you can always disable an alias file, and then even if it gets updated it won't affect you.
now to your other point:
I would prefer a clean installation, without plugins and without aliases (just keeping existing personal).
i've been debating this back and forth with myself for a couple of weeks leading up to farr 2 release. i am leaning towards making it a lean download without any plugins, but making it really easy to install new plugins using the updater tool. Inlcuding alias files is not as tough a decision since they are so small and lightweight..