In the latest version of mojoPortal it is possible to assign categories with "Show Categories" unchecked.
Yes, the plan is to be able to edit layout.master as well as CSS, though there is great potential for users to break things by making mistakes in layout.master. Any mistake in that file and it will fail to load it and fall back to a failsafe layout.master. There won't really be any good way to validate the layout.master, at most we can maybe test if it throws an error, or we can add something into the failsafe layout.master that gives information saying it failed to load the intended layout.master file.
Best,
Joe