Dale,
I haven't tried modifying any of the CMS 7.x reports (finally got my 7.1 test box set up this week!) but if they are anything like the reports from Patch 6.2...I suggest putting on your SQL hat or calling a pro. In 6.x at least most of the reports were generated by DB stored procedures that shouldn't be modified (though you can copy the code out of them into a report, or another custom stored procedure of your own). What may work is to execute the results of the built-in reports to a temp table, then run a select against that to filter out those which are Unclassified...but that won't help much for compliance drill-downs and global percentages.
As I get more into 7.1 and figure out the inner workings, I'll post back if I come up with something. Does Custom Severity still exist in 7.1? Would that help you, to flag those Unclassified patches as your own custom classification, like "excluded" or "not approved" or something?