LLCs are normal for CRE, so you divvy up the ownership interest how you and your capital partner(s) see fit.What's your specific question? 

What would one of you suggest for a medium term operator whose tenants may be over using a specific utility like gas or electric.

A HELOC on your duplex or home offers flexible, low-interest financing ideal for BRRRR, with potential tax-deductible interest if used for property expenses.

Is my accountant accurate in stating I cannot deduct the expenses related to the property if it's not listed in an LLC?

This is also tax deductible.

Finally, short-term rentals can offer potential tax advantages, as many expenses associated with the property may be deductible.

If they work independently, set their schedule, and use their resources, they might qualify as a 1099 contractor, but misclassification risks IRS penalties.Wages for W-2 employees and payments to 1099 contractors are both deductible business expenses, but compliance is key.This post does not create a CPA-Client relationship.

Even with the redactions, it's not hard to figure out based on deduction how much we are making from the rental and from my income.

Nate @Nate Marroquin   You can use the income from your tax returns on the current rental adding back your paper loss (depreciation) and add back the mortgage interest, property taxes, home owners insurance deductions on your tax returns. 

If you want real rental history for your specific neighborhood and data points on appreciation of your area specifically, let me know.