First, it is important to differentiate membership into two Houses and having House virtue from two different Houses. Dual membership has political meaning - who is a mage reporting to (you cannot serve two masters...) and depending on the house, they can have a strong view on that point, and some could not care less (House Ex Miscellanea for example).
A good background, discussion with the SG and the flaw Dark Secret and/or Tormenting Master, I am sure many combination of house virtue are possible at character creation. Many other virtues can be gained through initiations, and gaining some unique house virtues (Bjornaer and Verditius) without House initiation can be excellent story materials.
What if an Ancestral Beast initiated a mage or an apprentice outside of House Bjornaer in the Heartbeast Outer Mystery for its own purpose? (I personally would recommend to keep the restriction regarding familiar, at it makes sense in the meaning of having a Heartbeast).
Since the Automata mystery has been leaked out of the House Verditius, it is the proof that for at least some Inner Mysteries, it is not needed to have undergone the Outer Mystery initiation (Embrace of Boetius), and technically speaking, the one being initiated does not need to have a high score in Cult Lore (in fact, it can be debated if even a minimum score of one is needed), only the Mystagogue needs to be knowledgeable. Considering how upset was House Verditius when the Automata mystery was leaked, the mage having Inner House mystery knowledge would need to be very careful not to be harassed by endless wizard's wars, certamen and very likely the full political power of House Verditius.
Enigmatic Wisdom can be gained through Twilight experience, and I am sure Criamon mage will gladly share their knowledge to who is willing to listen to their philosophy.
Mutantum magic is usually in Mercere House mage only, but despite their best effort, some genealogy tree might have been forgotten, and a few generations later a apprentice, taken by another House mage, might start to show Mutantum abilities. If those abilities are confirmed a few year prior Gauntlet, when the apprentice is the most useful for his master, said master won't let him go, so he will be Gauntleted in another House. It is possible that later, House Mercere is going to approach him to join the Cult of Heroes, or even switch house. All that is good story seed material.