I've only ever purchased homes as primaries, one being rented out currently to an insurance company and the other is my current primary.

The current use of the property as a two-family dwelling significantly impacts its value and marketability, which is distinct from single-family homes.The initial appraisal comparing your property to single-family homes is likely an oversight, as multifamily properties are evaluated differently due to factors like rental income potential and investor interest.

They may require a foundation (footings) of some sort, a different home set up, among other things.

The honest answer here is in this marketplace not knowing what you're doing the risk is high.Knowing what I know now on the forums is totally different.

If you are talking about NYC investing, that's a different setup, not as streamlined as Westchester.

I moved here from Florida after doing a ton of research on different real estate markets. 

Buying a house is straightforward; managing it can be a whole different challenge.

You might find that installing a mini-split system, properly insulating, and ensuring the finishes match the main home’s quality will make a difference in how the appraiser views it.

Diversifying into different markets, like Omaha or Austin, can help reduce any lender concerns and also spread your risk.Have you thought about the specfic market for your STR or MTR?

They are good for comparison of different assets and limited in telling you when, where, or how to invest.