Ask them what the max square footage extension a new investor can add to a property.Ask them for their DSCR (long-term) chart, see if he/she can produce one.Ask them about their closing requirements for title agents, ask to see it.This is a good list for any new investor to shoot at a perspective lender. 

Yes there is less square footage, but a new toilet is still a new toilet. 

Sounds like you are perfectly fine.Having surprise extra square footage is usually a good thing, if you can finish it off.

I know of no investor in my market that would not purchase a duplex that is 3/1 versus the same duplex 2/1 if the price was only $5K higher (both duplexes in this case are same condition, footage, and similar locations but one has a floor plan to have an extra bedroom versus the other floor plan). 

The common charges and taxes keep going up, there are several assessments, and I'm pretty limited with what I can do with the unit as far as adding value.With a multi family, you can rent one unit out, make condos out of the building, add sq. footage, convert to large single family, really endless potential. 

Back when I was dealing with this, the non-permitted square footage was valued at 50% of market value.

Some appraisers are a little bit more generous with a "condition" adjustment, however the features that carry a larger monetary adjustment are garages, porches, square footage, etc...If the subject property has the same features (or less) than the comps, then new kitchens/bathrooms/interior may not add enough value. 

Or you might be adding an addition to add livable square footage and build a lot of equity.

The selling agent should not be counting it as livable square footage.

Renovation, updating with LVP throughout, increased bathroom square footage, all new bathroom, improved the "flow" of the floor plan by creating an "open concept", added washer/dryer hookup, general upgrades, finer finishes.