This letter is designed to give pause to (e: previously I wrote "kill") a company operating with complete disregard for proper operations in a regulated industry.
We are in entire agreement, but people cannot believe in the superposition of this and "Oh that's just some simple questions from the regulator."
Edit to add: Quoted bit appears to have changed after my quote. I think the old version remains accurate.
I originally wrote "kill" to mirror your original comment, but I changed it because it (as I perceive the word) presumes a level of intent that I don't think NHTSA operates with: I don't think that NHTSA has any intent to destroy this company. In fact, if comma.ai reached out to NHTSA, I would expect NHTSA to assist (within reason) in answering the letter.
I do think that these are straightforward questions for a group that has its act together. Part of having one's act together in a regulated environment is maintaining open lines of communication with regulators, so that questions would be asked should come as no surprise. Keeping up to date with the regulatory environment would also be expected, and given the recent autonomous driving publication the content and scope of these questions should come as no surprise.
If these questions kill the company, I don't see that as being the fault of NHTSA, I see that as being the fault of whoever is in charge of regulatory affairs at comma.ai.