Just a small reply to what you're asking... I've tested it with a Kingston 16gb CF and it worked :-)
I really see no reason why anyone would want to change the menu, it's nice and slick looking - kept simple which is awesome.
Also, no saves ever saved on the "N64 itself", but on the cartridge of controllerpak. These cartridge saves will be written to the CF in a "saves" directory. Who knows what the future will bring regarding Controllerpak.
The 64drive won't let you down, it's so easy to use :-)