For example, if I make my own house, can I then ask followers to move and even marry? Or are these features only available in vanilla houses only?

I think there needs to be added a provision for the follower to know that is the home. Because, when you send them home, they need to know where to go.

I will move this to the Editor section as that is where your answer lies.

I believe some of the follower overhaul mods add support for setting custom houses as your home.

Then again, there's always http://skyrim.nexusmods.com/mods/18045.