You do realize it says they MAY have one humanoid subtype, right?
Right after it says "IN GENERAL,"
Subtype limits and restrictions are quite clearly being pretty vague on the limits and restrictions.
Because they didn't think of situations where one could have multiple humanoid subtypes, but also left it openended because they probably thought they might've missed ways that one could. I unno. *shrugs*
As you stated, it ignores creatures with multiple energy subtypes because the quote says "one energy subtype,"
Because "IN GENERAL," is generally "Usually it's like this, but it doesn't always have to be"