The UI is handling the update of the quantity for tag-along. With POS, when you add an item to a transaction it somehow remembers that the tag-alongs are linked to the first item. So when you change the qty of the first item, the UI goes and changes the qty for the rest of them. When you recall a transaction, the UI does not check for this link, and so each individual transaction entry is treated as a stand-alone item. I guess you could consider it a bug. You could open a support incident about it, so that they can fix it.
As for how this affects your add-in, it just means you need to check for tag-alongs in your code. I'm sure they left it up to the UI on purpose, rather than letting QSRules handle this.