I'm not clear as to what you're referring to when you say, 'aren't crawl spaces dug lower than block foundation?' That's for starters. But, neither here nor there, let me share this w/you.
The block should be on a poured footing. The footing's depth depends on the frost line. It should be below that. Then, the block foundation can be built on top of that. Now, one could pour the footing AND the footing at the same time. In fact, they can be the same depth BUT you want to be sure that water infiltration issues are addressed. In other words, if the footing and the foundation were at the same 'level', then water could EASLILy end up in the crawl. So, a french drain needs to be added, possibly along with a sump pump.
What I'd do is this. Talk to the builder to find out exactly what he's gonna do. If he's reputable, I'm pretty sure he isn't gonna do anything that could end up in court. Just get his 'fix' in writing and be SURE that his fix is what was written. Let me ALSO add this: For a few hundred $$$, hire yourself an ASHI-Approved Home Inspector for the building process. Find an inspector that's VERY Familiar with new home construction! Have HIM be sure the builder is doing the right thing. Understand that the Inspector is NOT your General Contractor. Talk with your Inspector to insure that what's been written in the contract is being adhered to. Also, he should be making a number of 'visits' to the job site during the process. He should be there (in the least) when the footing and foundation are formed, the home is framed, the home is wired and plumbed, the home is finished on the outside and the roof is on, and when the inside is finished. These, again, should be a minimum. For the $$$ it costs to have someone looking after YOUR interests, that's cheap when you're talking 10's of 1000's of $$$s, perhaps 100's of 1000's of $$$s over 20-30 years. It just makes good sense! Visit the ASHI Web Site and read about how to choose a Home Inspector. And read the other stuff too.
This, in my mind, is how the 'common person' can better protect themselves to ensure the work is done properly. (Hire someone that's looking after YOUR interests.) My best to ya and hope this helps.