In a table view column "A" is the unique value count in a aggregation. Is there a possibility that I can filter on this newly generated value instead of the underlying values in the database?
Only for the underlying data. This would not reflect the effect of your filters. It would only represent the unique value count in the full dataset. (It is not possible to have the unique value count *after* filtering to itself be filterable.)
One way to do this would be use an Aggregate block in DataManager and merge the results back with the granular data. Another option would be to define a formula field as SUBSET_UNIQUECOUNT.