I would think they would find the difference during the rebuilding process, no?
That's my thought. The 5th gen caliper pistons are larger than the 4th gen, so the 5th gen caliper pistons won't fit in the 4th gen caliper body.
So if they tried to rebuild a 4th gen core using 5th gen parts, at some point, they would find that the pistons don't fit, and that would let them know that something is wrong.
I assume it's more likely that their process is to clean up all brake cores using whatever process they go though, then read the casting numbers to identify and sort the parts, then line them up to be rebuilt using the correct parts based on the case numbers. That would seem more logical to me.
For example, suppose a customer returns 4 cores, but gets the tags swapped so that they mislabeled and accidentally swapped the tags on left front and the left rear calipers.
If the rebuilder simply rebuilt them as tagged, then repackaged them and resold them as they were labeled when they came in, I suspect that they would have large numbers of inventory errors, and many upset customers.
I don't see how a company could succeed relying on that process. I would think that they would HAVE to check the casting numbers to positively identify a component. After all, when they sell the reman part, it's THEIR reputation that's on the line.
More likely is that compared to the number of caliper replacements on 4 runners, the people doing the upgrade swap are a small percentage and over the long run won't make much of a difference... especially as the 5th gens continue to age, so more and more 5th gen's get scrapped and have parts remanufactured. The upgrade crew might have put a slight supply shortage on the 5th gen replacements for now, but that should ease up over time.
Also, the remanufactures probably don't even care. The 4th gen cores will be remanufactured as 4th gen cores and resold to other 4th gen owners with failed calipers who don't upgrade. We all know there will be no shortage of failed 4th gen calipers!!!!
Just my $0.02.
-Phil