One possible work-around for this is to create duplicates of the fields that are used for the drill-through filters and then only use those fields in a particular context.
For example, let's say you have drill-throughs for an "Expense" report and a "Revenue" report that are based off the account name, but you only want to show the Expense drill-through on your Expense summary visual and you only want to show the Revenue drill-through on your Revenue summary visual. To get that behavior create duplicates of your account name and call one "Account_Name_Expense" and the other "Account_Name_Revenue". Only use Account_Name_Expense in your expense drill-through and visuals and only use Account_Name_Revenue in your revenue drill-through and visuals. To users the displays show the identical account names, but the drill through options will be different.
This is still just a workaround and I encourage people to vote for the suggestion to make a proper drill-through control.
