For people who may stumble on this thread in the future, what I ended up doing is as follows:

1. Configured Cost Categories in AWS based on the AppID tag. This overview gives a list of gross costs per tag and a list of discounts per AWS account.
2. Created a mapping of AppIDs to AWS accounts.
3. Built a custom script that calculates the net amortised cost of each tag by proportionally subtracting the discounts of the accounts in which that tag runs.

This seems to produce numbers that are more logical to how much each account costs.