1. You do not know the garage was not permitted, from your own post, as you don't know when it was enclosed. Could have been done before records retained. Therefore you have to assume that the permit was issued.
Why does an appraiser "have" to assume a permit was issued, when they have no way to find out? (and, if, after all these years, the garage conversion is not on tax records GLA, the evidence is more that it was never indeed permitted)
2. What code requires now is not relevant to a dated enclosure as the enclosure would have been done per earlier code requirements.
The enclosure might have been done prior to a code, however, if it is not up to current codes, it is not. Just report that. Let lender make the decision about whether to lend, but they should know condition of property and whether it conforms to others in the area or present safety and building standards.
3. If the enclosure is of the same quality as the residence, it is GLA. If not, it is valued separately.
Not sure about that...certainly it is square footage, whether or not appraiser includes it in GLA is another matter...the appraiser can, but to say it has to be done that way? Whether or not it is included in GLA, appraiser should disclose and describe the living area and how it is used, and if market is returning value, the value can be on report whether or not the area is part of GLA
4. Congratulations. You now have opened yourself to liability, revealing confidential information to the building department.