You think designing and manufacturing a new MCU would be cheaper?
Paying someone to refurbish the daughterboards by replacing the $5 eMMC isn't going to cost that much. It is probably less than an hour of labor.
Absolutely. In the volumes we're talking about, where the boards you need to repair are spread all across the world and you have to get the work done in some modest amount of time?
You've got to pull the board, pack it up, inventory it, ship it back to a refurbishing depot where they'll have to unbox it, inventory it, diagnose it, repair all the things wrong with it, validate it, ship it back to either a central depot or whichever service center needs that part (hint, all of them).
Assuming you've got a shop that can grind through 500 per day, the simple "diagnose / repair / validate" cycle is going to require people with specialized skills, specialized tools, and an inventory of replacement parts. That's a reasonable thing to do if you're doing 5 per day, but scaling that to hundreds requires lots of people, tools, and space, and at the end of it you're not really 100% sure the result is going to be good enough to actually satisfy the NTSB. It's a bit like betting you can make an Audi Allroad with 190,000 miles work. Sure, it's just "repair work" but who's to say it isn't going to throw some other weird error 5000 miles after you've replaced the air suspension (again)? (In this case, I'm referring to "what if the flash storage isn't the only underspec part, and the touch screen controllers also fail at some rate high enough to cause the NTSB to reopen the case because they've gotten 8 complaints on your "reworked in a shop in Tijuana" parts)
The alternative is to make a new board, which involves farming the design out to a shop that specializes in that, then take the prototype that shop and make sure it does what they say, then send the design to one of hundreds of shops in china that specialize in that sort of work. You take a one-time hit to your bottom line and move on.
Scale changes everything -- a program to keep 10,000 spares in the warehouse by refurbishing / reworking the small number of cores that come back to you is radically different from "we need 150,000 and a plan to keep the feds off our back"