So Apple finds a defect but will charge people who's warranty has expired?
The fault doesn't seem to be an increased failure rate, but when one part goes so does the other. Without having exact knowledge as to why, my guess is they're somehow paired together the way Touch ID and MLB are.
The flat rate out of warranty cost does not change if just SSD/MLB or both SSD & MLB need to be replaced.
This internal memo doesn't effect the public that much, hence why it's internal. It's to help the Geniuses correctly allocate parts for a repair.
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I can't imagine that would fly in any EU country. Sure, one or other could fail, outside warranty. But having to replace two expensive and (normally) relatively un-coupled components when only one fails, sounds like a flaw. Any customer would have very strong grounds for challenging this.
The charge for MLB & SSD is already the same cost as MLB or SSD separately. This will cost affected customers no extra money even if out of warranty.