Or it could be artificial like bad pictures, scrubby yard, or some other $1,000 problem.

He is a family medicine resident so we're seeking a physician loan as opposed to FHA in order to avoid the PMI that comes with a low down payment. 

When investing 50-60k you ve got 2 optionsIn an area where property value won t go up and the rent won t be high(but probably low tax and low hoas)  or a smaller property but where the value will go up and rent will be higher (but higher tax and hoas).In the 1st option, it will never change until a major real estate investor makes a deal with the city and decides to turn the area into an upscale one.In the second option, you are already making money; on today s market I ve sold a few units of mine on which the return is at 8% net and the value of the property is going up 15-20% each year.What you don t want is flip the property too many times in the course of 2-3 years, because of the real estate commission that as a consequence increase artificially the market price and decrease terribly your margin/gains.If you sell 70k from which you substract real estate commission(6%) and title fees, you ll end up with less money to buy a similar property that therefore you won t be able to buy(or re-invest in that case); so you ll be losing money and only the real estate agent will be making money.

Other times a new $120 vanity with drop in bowl sink and a new $50 mirror instead of a sink from the 50s and a medicine cabinet can elevate a bathroom.

You are basically going to pay points directly or through seller credit to artificially lower the note rate 2% in year 1 and 1% in year 2.   

It is likely that your property tax is artificially low due to prop 13.  

Be doubtful of science and the medicine at your own peril.  

So that 3 comps is artificially inflated the market,sometimes unnecessarily.The one that's really driving up the price is really inventory these days and/or the DOM.

Civil engineering, like medicine, has specialties within the profession and most sites require more than just one.

The rule book is here: https://www.fanniemae.com/content/guide/sel022316.pdf The tricky underwriting can come from commercial lenders and their risk mitigation people who have rules that seem arbitrary or artificial.