Water/sewer isn't metered separately for each unit and the garbage fee is lumped in on the same invoice.

Do you know how much it cost to install a separate electricity meter on a duplex?

This is essentially just paint at 1k per unit. i would want more than that but your inspection would tell you all you needed to know-in a 16 unit, they would be (should be) on separate electric meters, which would be billed to the tenants, not you.

I've been looking into sub-metering a SFH home with a mother-in-law suite and experiencing difficulties regarding zoning and the utilities companies.

That style of building usually has separate gas/electric metering per apartment, so the landlord pays water/sewer/trash.On the topic of your agent not wanting to make an offer, have you asked your agent to prepare an offer?

Are utilities separtely metered?

There's no real 'fair' way to truly separately meter the natural gas used for the different units, unless you get into rabbit hole land of re-inventing a wheel and a series of sensors measuring heat and air flow within separate ducts, on your (customer) side.I'll comment on each option individually and your decision will be numbers driven. 

Is it feet, yards, cubits (LOL) city blocks, water-meters, utility poles, sewer lines, or just plain up to the lender?

Many large apartments are master metered and are constructed in a way that prohibits a company from going in sub-metering them.

The home does not have separate meters for gas/water/electric and all the ducting is connected to the same furnace and A/C... the thermostat for the air conditioning and heater is in our unit.