One issue is what happens when one of the copies is removed, especially if there's more than one owner involved. Presumably the result must be that removing a file can increase someone else's quota usage. One wonders then what should happen if that other user has already exhausted their quota, and what bugs may be triggered by not expecting whichever policy is chosen.
The reasons for different quota behaviour would be if it results in different (and more desirable) user behaviour, or if it helps system administrators choose better quota limits, i.e. if it results in less frequent filesystem-full situations for a given amount of user productivity.
How much are quotas used these days, and for what uses ? Can people comment on the usefulness of different quota policies in the context of specific use cases?
As to whether different quota behaviour would result in different user behaviour (e.g. encouraging taking steps for files to be reflink'ed rather than copied), I wonder how many quota'd users would have the necessary knowledge for it to change their behaviour.