It is a tri level house that sets up very well for house hacking with three separate common areas and a large backyard.

Common to find 70%-75%.

This agreement does not prevent you from making a passive investment in any publicly traded securities so long as such investment does not confer upon you or any entity that controls you, is controlled by you, or is under your common control of 5% or more of the outstanding securities of any such entity as described above.

Hi @Aaron PopeCongrats on the first post and welcome to BP, your life will never be the same:)This my best advice, and a common thread from experienced investors here on BP.

Sunken Master Bedrooms or Living Rooms are somewhat common, and shouldn't be a big issue.

Is this common practice, or do I need to find a new company to work with?

I'm going to guess that it is held as tenants in common - your husband and his sister. 

Just wondering with this vast number of people on this site if anyone has ever had this happen to them and is this really common?

You do see it in Boston, increasingly more every day, but that's the only place I've seen it commonly in this area.

It may not have a swimming pool and common amenities but good quality construction.