What some people do is just not launch that particular window through Inner Space or ISBoxer. Then it's a no-brainer
What you're looking for, though, is the Repeater Target. By default, the Repeater Target is "Window:All w/o Current" meaning that when you flip on Repeater ("Broadcasting") your keystrokes and clicks go to every other window and fall through into the current window. In this case, you want to replace "All" with some Action Target Group containing the 3 you want.
So to start, make an Action Target Group. Right click on Action Target Groups in the top pane, select New Action Target Group. Name it something short and sweet that makes sense as a logical grouping of those 3. Like... hulks or something. Drag the appropriate Characters from the top pane, into the Action Target Group in the bottom left pane. Then you're done setting up the Action Target Group. It's just a subset of your Characters.
Now you need a Mapped Key that has a Repeater Target Action. If you WANT, you can just add a Repeater Target Action to the existing Activate Repeat mapped key in your "Always On" key map created by the wizard. That would require the least amount of work on your part, but without making a separate key it's just always going to work like that. Maybe you want it to always work like that, maybe not, I have no idea

I'll go with this for now. In the top pane, select Always On under Key Maps. Then in the bottom left pane, expand Activate Repeat so under it you see Steps, 1, 2. Click on the 1 under Steps. Now on the right, you should see a box that shows Step, Actions, and some stuff under that. Right click Actions and select New Repeater Target Action (under the Repeater Actions submenu). This Action has 3 settings: Target, New Repeater Target, and a checkbox that says "Block buttons from originating window". Set Target to "Window:All w/ Current", this will make your new Repeater Target apply regardless of which window the broadcasting source is ("originating window"). Set New Repeater Target to "Group (others in): Hulks", and leave the box below it unchecked. Finally, move this Action to the top of the Step; to do so, right click it in the Actions list and select Move Up. (ISBoxer 38 adds a quicker method by pressing Alt+Up and Alt+Down, but that's not live yet)
If you followed this line by line, you now have what you asked for. To be clear, if you want to reset it to the original state you would want another Repeater Target Action that sets the Repeater Target back to "Window:All w/o Current" for all of the windows.