When a nonconforming lot can be used in conformity with all of the regulations applicable to the intended use, except that the lot is smaller than the required minimums set forth in Section 15-181, then the lot may be used as proposed just as if it were conforming. However, no use (e.g., a duplex) that requires a greater lot size than the established minimum lot size for a particular zone is permissible on a nonconforming lot.
Well in that particular case the use (as a 2 family) is prohibitted due to lot size so it would be checked as either legal non-conforming or illegal depending - but it remains a use issue. In fact, the way I read the ordinance, I am guessing there is a separate minimum lot size for a 2 family in this residential zone, so even some lots that meet the minimum lot size for SFR cannot be improved with MFR, unless they get some type of approval.
But I am not saying that lot size requirement is unimportant. Nor am I saying it should be overlooked.
If you have a single family residence built prior to code, in the zone you are talking about, and it does not meet lot size requirements but, as you state, the use is permitted, are you checking "legal non-conforming"? Personally, after reading Fannie, I don't think you should because that section of the form per the guidelines is concerned with the legality of the use and your use is legal. But if the house you are appraising is a two family and the circumstances are otherwise the same, then, based on how I am reading the guidelines, you have to check legal non-conforming or illegal, depending.
Of course, either way, you are responsible to determining the effect on value of having a lot that does not meet minimum lot size requirements. If a lot is undersized, or if set backs are not met and I can tell, I put that in the site comments and look for similar properties for market reaction. But that alone doesn't make it a non-conforming use.
Just like you, I include the zoning ordinance on rebuild directly in my report when necessary. It is easy here. Just a cut and paste off the internet.