Actually, I don't think it's the act of creating the sdkregistry directory, but the act of creating a tomtom.mnu file there with new commands which builds a new set of menu screens. Since we don't yet know the commands for the Help Me and Map Share features, they can't be included in tomtom.mnu, and they get lost.
Installing Suntime doesn't do this, it just automatically gets inserted onto its own new menu page. I experienced the same thing after installing Offroad Navigator -- the stock menus stay put, with a new page 3 for the new app.
Hope that helps -- I'm a newbie here, but I think I got that straight!
I think you nailed it.
But I was correcting the previous poster who said that creating the sdkregistry replaced the entire menu system. I was also looking to explore/discuss a third possibility...
Instead of creating a tomtom.mnu which replaces the whole system, why not figure out how to create a third menu page much like Suntime does? If we know all the commands (except for Help Me and Map Share), why can't it be done like that? You know, leave the stock menu pages and add your new hidden features to additional pages.