You make a good point. I do think that ideally the pages can be stored as HTML or text files rather than text fields in database. The reason why it was originally done this way is that the custom pages themselves ain't complete HTML of the page, but only a portion of it. It's not a problem though, as a GUI Comment can take care of this now.
The CKEditor will be optional in Mys v1.4.0 and onwards. There will also be options to use a standard or full version of CKEditor. Take a look at these two links and you will know what I mean by two versions of CKEditor:
http://ckeditor.com/demo#standard
http://ckeditor.com/demo#full