When I place a character using the root template Humans_Hero_Male base, and then check it as global and modify it's base appearances (face/hair etc, using only already-existing ones), and do literally nothing else to it, in character creation the character does not have the appearance I select--just some generic appearance, and if I start the game with this character origin it remains in the SYS_CharacterCreation level and doesn't proceed to the Fort Joy tutorial ship (the character I made doesn't even go into my party and no menus are accessible).

No idea what's going on there. There must be something more needed than just checking Is_Global, and the GUID used by the template must have such settings, but you can't search in the editor by GUID that I'm aware of to look and see what other settings are going on.