The permanent fix involves soldering stuff on the mainboard, which I don't have any prior experience. The RTC substitute module you mention is just the ML220 coin battery that will also eventually stop working.
I did this repair and it was not nearly as easy as you imply. The wire is extremely thin, and the pad on the motherboard is extremely small. I had to purchase special eye-wear in order to see what I was doing, in addition to a soldering iron.
It was and is totally wrong that Framework requires users to repair a component that was faulty from the factory. You should ship the laptops back to your facility and repair them, at your expense. At worst, offer a substantial discount on a motherboard replacement.
This experience is a big reason why I went from a strong Framework proponent to a strong detractor. You do not support your products, and users cannot trust you to do the right thing. You now bask in the idealistic haze of nerddom but your actions show that you're just a business for whom repairability is a sales strategy to justify premium prices.
The warranty suggests that Framework would "ship the laptops back to [their] facility and repair them, at [their] expense," as you said they should. Did that not happen while your warranty period was in effect?
I appreciate the response, but my suggestion would be to offer a mail-in service program so that users don't have to fiddle with potentially dangerous soldering (ideally Framework bearing the shipping costs or atleast subsidizing it).