All of those questions can help your agent structure an offer that will be competitive against others. 

(Sorry accident hit post before I finished the sentence)

This may be where your initial disconnect was.Something else to keep in mind is your entity structure and how your entities file tax returns.

What are some potential structures to allocate direct expenses to the rental on primary residence property and keep the activities separate as not to pierce the veil?

Can be structured in a way that you retain maximum flexibility in ability to refinance, sell notes, or utilize as colterol for future endeavors etc etc.. 

How much of the structural part of the space is covered by the tenant?  

You have to be specific about what the deal is and its structure. 

CT requires an Architect (or Engineer) for projects of this nature, especially a building of this age where it's likely there's structural/framing items to address.

You should verify this with official HUD documentation or through a HUD-approved lender.Term Until 2051:The mention of the loan term extending to 2051 or until the property is sold or refinanced suggests these could be loans with a long-term structure or special conditions.

Best thing to do would be to contact a lawyer and have them help you with structuring the note.