As mentioned, it’s not FAA rules you break. The 2000’ is a NPS guidance trigger point that brings other NPS rules into play. Where the OP letter writer went wrong was to state the trigger instead of the actual rule like wildlife harassment.The FAA merely "advises" you of these other rules by requesting the 2000' with the AIM taking a step further with this:
View attachment 96461
There are several congressional acts that empower the NPS and other agencies to enforce their own rules with a number at the statue level. So the letter had the DOJ reference correct. The difference in the enforcement is the aircraft is merely the “vehicle” to violating the primary NPS rule, i.e., wildlife harassment, too noisy, etc.. It’s no different than if you use your SUV to chase a buffalo. These are also the same laws/rules that allow the NPS to prohibit drones in national parks where no one else can prohibit drones from other non-NPS public areas.
Regardless, if you fly below 2000’ over a designated wilderness, determined to have violated an NPS, BLM, USFS, etc. rule, and they can identify you, you may be surprised at the outcome. But if you do get caught don’t use the “aircraft emergency” excuse unless you actually have one and follow the applicable FARs when you do. Trust me.
FYI: The Part 136 tour regulations were in response to the mountains of complaints made to the FAA and Congress on aircraft noise in wilderness areas. The only thing the previous government studies did was make it easier to pass. The tour operators were a distinct minority in the process. There was also a movement to include private GA flights as well but it was stopped at the “commercial” level. But given the FAA still fields numerous complaints on aircraft/drones in wilderness areas every month, the ability for the average person to do so will go the same route as tour ops and the FAA will be publishing FARs to regulate that as well.