Flipped homes use flipped comps. The system just feeds itself. We did a flip back in 2009 when prices were going up and had offers way above what we thought the home would appraise for. The VA appraiser was able to use recently closed flipped comps and looked at the multiple offers (22 offers above list price). The VA appraiser was also able to factor in the mandated seller concessions.
I have talked to other flippers about getting the appraisal numbers needed to close. They prepare a list of work completed and hand it to the appraiser.