Should I consider them when comparing other applicants? 

Remember people who look at your unit have probably looked at  many others. they have a pretty good idea how yours compares.

Since there will not be that many compared to SFHs the cost may be reasonable.

Hi Daniel,I think what I have been seeing for the most part is that duplexes up to four plexes are not necessarily marketed at certain cap rates but whatever the market and comparable properties have been selling for.Maybe a factor that contributes to this is that anyone with a traditional home mortgage can purchase up to a 4 unit building without getting a commercial loan.

Like a traditional refinance into a 30 year at a lower rate?  

@John MerrittSacramento is a unicorn market when it comes to rent growth and appreciation, because you have a large population moving here from the Bay Area where rents and home prices are 2-3x as much for comparable properties.

Once we 'assume the contract', how does that compare to a typical escrow?  

Please any advice would help $50k can get you $200k worth of real estate using traditional financing.

All in all, I would compare the two and see which one works best for you. 

You really need to balance the opportunity cost of the interest you'll save with the returns you can make by investing that $400/month or however much you can scrape together.If you want to get real nerdy, you can download a loan amortization spreadsheet, plug in the extra payments, compare the interest saved each month versus what it'd be if you keep the loan as is, and discount the NPV into today's dollars.