I think it's purposely not defined for DM's and players to decide what works best for them.
Not much help as far as rules go, but most of the unchained stuff is sorta stuck in an "as is" state like most of the other alternate rules systems.
I see these optional rules as suggested house rules. So it's not like they are official core rules.
I see variant multiclass and counting fully as class of that level as the text suggest but doesn't out right say.
"With this system, each character can choose a secondary class at 1st level that she trains in throughout her career, without giving up levels in her primary class."
So secondary class is level is that class in my book.