Pretty certain that processing rules get processed before the uniques limit is applied to a variable otherwise things that don't have the uniques limit applied (e.g. data warehouse, data feeds etc.) would have some serious issues.
FYI - don't know if you are aware but the default uniques limit is 500K but you can get this raised to 1 million just by contacting Client Care (and if you ask your Adobe account team very nicely they might let you take it above that).
