First, you can't talk about these issues without first getting past local code. The Pacifica Planning Department has very specific garage regulations. And in fact, with all the zones and exceptions, they are fairly complex. But. you have to deal with them.
Generally, SFR houses built or updated since 1988 have to have a two-car garage. My 1953 home had a big addition in 1993, and I had to extend the garage with another bay. Unless, for some reason, you are exempt, you cannot convert a garage bay to a bedroom - or any other non-garage room. People do. I did. But if you sell the house, you will have to convert it back. So you probably erect an intermediate "knock-out wall." - So the appraiser never counts a garage as living area unless, for some reason, the planning department approved the conversion and it passed final inspection.
All this going to the planning department, or possibly online to check plans, approvals, and inspections, takes time. And I am pretty sure a good number of appraisers don't do the work. Remember that Black couple who sued the appraiser in Marin County for undervaluing a house they had remodeled? They never got through the final inspection. And none of the appraisers caught it. But I found all the records online, clear as day. Even after they won their lawsuit, they didn't make the effort to get the upgrades through final inspection.
Anyway, if that first story is above grade, then all ANSI-compliant finished living area would qualify as living area. If it is partially below grade, and the house is backed into a hillside, it may still qualify - but I would recheck the latest GSE Guidelines on that.