Let's go down the documentation rabbit hole for a moment.
91.417(b)(2) tells us which records must be retained and transferred with the aircraft:
The records specified in paragraph (a)(2) of this section shall be retained and transferred with the aircraft at the time the aircraft is sold.
What are the records in paragraph (a)(2) that relate to alterations, you ask?
Copies of the forms prescribed by § 43.9(d) of this chapter for each major alteration to the airframe and currently installed engines, rotors, propellers, and appliances.
So, what are those forms prescribed by 43.9(d)?
In addition to the entry required by paragraph (a) of this section, major repairs and major alterations shall be entered on a form, and the form disposed of, in the manner prescribed in appendix B, by the person performing the work.
Now, then, we've almost reached the rabbit at the bottom of the hole. We finally take a look at 43 Appendix B(a).
Except as provided in paragraphs (b), (c), and (d) of this appendix, each person performing a major repair or major alteration shall—
(1) Execute FAA Form 337 at least in duplicate;
(2) Give a signed copy of that form to the aircraft owner; and
(3) Forward a copy of that form to the FAA Aircraft Registration Branch in Oklahoma City, Oklahoma, within 48 hours after the aircraft, airframe, aircraft engine, propeller, or appliance is approved for return to service.
Stringing all this together, we see that the only record that must be retained permanently and transferred with the aircraft is a copy of Form 337.
There is no mention of any need to retain the permission letter.
As far as I can tell from the regs, the FAA has not authorized, much less empowered, IAs to act in the role of intellectual property cops. As you state, that's a civil matter, and there are civil courts to deal with such things. The role of the IA is inspect the aircraft for conformity to the type certificate and to alterations/repairs documented on the 337 forms. The mother-may-I slip is not necessary to determine conformity, nor is there a requirement for the owner to retain and produce it.
If there are FAA rulings or legal opinions to the contrary, I've been unable to find them. If someone can produce something official from the FAA that clearly requires retention of the permission letter, I'm perfectly willing to change my opinion. (But if you can't find it either, for Pete's sake don't ask the FAA!)