The appraiser threw out an unpermitted unit that has rented at $1,400 for years

Duplex, contract at $410,000, lender ordered a 1025. There's a converted garage unit that's been rented at $1,400 a month for years, no permit on file, separate meter, own entrance, kitchen and full bath. The appraiser excluded the ADU from GLA and from the income analysis, treated it as garage space, and came in at $385,000. The rent roll the seller gave me is $3,900 a month total, so almost 36 percent of the income is invisible to the report and the DSCR math the lender is running.

What I want to understand is the mechanism, not the outcome. Is there any circumstance where an appraiser can give contributory value to unpermitted space, for example where the local zoning allows the use but the paperwork was never filed and the market clearly pays for it, and does that need to be a legal nonconforming determination from the jurisdiction before the appraiser can rely on it? Second question, if I got the unit legalized after closing, does that ordinarily require a new full appraisal to be recognized, or is a completion report enough? Third, would a private appraisal ordered by me on a market value assignment reach a different conclusion than the lender's file on the same facts, or is the exclusion driven by the lender's own guidelines rather than by appraisal standards?