OK, I see. There is no way to directly access the filters of the clips inside the transition once you have broken the relationship between the transition and one of its neighboring clips. I doubt that will change. Rather, if people are burned enough by this, then I will likely make a change that removing a clip next to a transition automatically removes the transition since people are also asking for better transition removal behavior. However, it seems others specifically want the current behavior:
You can’t please all of the people all of the time. So, yeah, here you need to use a workaround: delete the offending item and recreate it as you would like it.