First, you are assuming permits are required. Not always. I had to have a permit for my septic system, but there's a lot of homes in the area that had septic systems put in before the permitting was required. Not my problem, just cite that they're there and typical for the area. I do not call for permits, inspections or anything else (except FHA). That's not my business. If sewage is perking up through the grass, then I so state it. Again, an observation.
Second, you are making a lot of assumptions about pumpage, etc that are not nationwide. Your concern about allowable pumpage may affect a dryland farmer or major user of water, but that would be a local issue.
Third, not all restrictions are readily disclosed. Some of these obscure restrictions may not be readily available to the appraiser. I am an appraiser. I do not perform title searches, or other similar inspections. It's not my job. If there's something on the title search, then the buyer should tell me or the broker. I ask the owner if there's any restrictions. If everyone says no, I am not going to spend 5 hours at the courthouse researching the title to see if there is a problem. Again, it's what is readily available through public records.
That's just the way it is.