About two weeks later, the new geotech engineer and my structural engineer met and worked out that there should be a mat-slab foundation for the house. This means that instead of just having a perimeter of concrete holding up the full weight house, a slab of concrete will be poured over the entire footprint of the house to help distribute the weight. I was told the previous spread footing foundation would have most likely been sufficient, and wost case is I would have seen some very minor cracking over the years. The new foundation won't have this problem at all. That makes me feel better, especially for such an important part of the house.
The improved foundation uses more concrete and is more expensive, so the cost of building the house went up, but not by much relatively speaking. There is an additional benefit, however, to having a foundation of this type. It creates a very large crawlspace under the garage with a finished concrete floor. This opens up the possibility of using this area as a mother-in-law unit at some point in the future.
The revised plans will be submitted for post-permitting, and it won't hold up construction. The city is estimated to charge about $600 approve the revision to the permitted plans.