I wonder if messages rejected via the .mailfilter somehow count against the quota, but then are never purged?
No. Only messages that are actually delivered to a maildir get counted towards the quota.
Of course, if your .mailfilter file deliveries multiple copies of the message, each copy counts towards the quota. If your .mailfilter delivers a copy of a message, but still exits with an error code that causes a bounce to be generated, the delivered copy of the message still counts towards the quota.
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