Any sort of non-conforming use carries greater risk than if you're in conformance.Duplexes and SFRs are appraised in the same way - comparable sales. 

How could I conform to this, and the codes against unrelated people if I don't bother to ask?

Here's a way to think about embarrassment that works for me:Societies make their members conform in different ways -- there are always enforced limits placed on their members' behavior.

Is it because now it's a conforming bedroom with the new closet?

Zillow isn't the best but if you're in a conforming neighborhood a Zillow valuation would be a decent gauge before initiating a real estate agent to work on your behalf.  

There is usually a clause in the P&S or addendum to the effect that if the seller needs time to remove any defects in title, deliver possession or make the premises conform, you agree to give them an extension and if they are unable to perform by the expiration of the extension, the seller will refund buyer's EM and the contract will be void with no recourse to either party.

Hey guys, im a new motivated investor,i am 20 year old and im looking to buy a rental property in the future but where i live 90% of the rentals do not cash flow and if they do, they are D class property or non-legal/non-conforming duplex/triplex. 

A commercial lender would probably look at that more reasonably than a conforming residential lender. 

There is no limit to the number of non-conforming (fannie/freddy) loans you can have.

FNMA's conforming is not going to work with a buy price of 1.1MM and rehab of say $500k.