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

Unless it's been on two separate meters since it was r6, in which case there's a grandfather allowance.

The city quarterly bill has broken down the expenses into separate water and sewer costs, and the sewer is hovering around 400% more than the water.

Those two stay separate so you have receipts for your CPA and income/expenses is not "muddied."

The property is currently listed on the MLS as two separate properties when they are actually both sides of a duplex. 

I would advise opening a separate bank account for the real estate related activities if you are treating the real estate as a rental.If it is 100% a personal residence, no need.

This has the benefit of letting me immediately start renting out both sides of the property (after cosmetic repairs).Or I could purchase the duplex as a House Hack opportunity using an FHA loan with ~3.5%, down, receive a lower overall interest rate, and use the remaining funds to purchase an additional rental property, separate from the Duplex to increase the overall rental property portfolio. 

of a larger piece of property.So when they sell they can stay together and do one 1031 exchange to purchase new property together (they will both have to be on title of the new property initially).Or they can separate and each one take their 50%. 

That wouldn't really be house hacking, since you can only have a family member living in it, not a general renter, and you also can't pass the unit on to a subsequent owner automatically - they have to apply to the town and be granted it for their family member, separately.

I am fairly certain that zoning has been amended to not allow new separate structures for living purposes - must be an attached addition.