Welcome to the Autodesk forums!
The technique you've describe here is a good one, but the View Filter's color overrides WILL still hit the Detail (or Symbolic) Lines within the Family, not just the model elements.
I do this all the time. Are you sure you used Symbolic/Detail Lines inside of the family to represent the clearance? I attached a pic of one of my vav's colored by filter and still showing my dashed red line to symbolize clearance. Let me know if you are doing the same steps, or upload a simple family that is not working as I have described and I'll take a look at it.
Attached is a sample project with a Mechanical Equipment family (including Symbolic Lines), and multiple graphical situations. Revit MEP 2013.
I just did it here from your own file. Is this not what the Thread Opener desired? Perhaps I'm confused as to what he wanted to accomplish. Let me know if I shoudl also upload the .rvt.
OK, I see. So you set the View Filter to override the Projection/Surface Pattern, right? Based upon the OP's attached image early in this thread, he's aiming to change the Mechanical Equipment's Lines to brown, whist keeping the Lines of the clearance zone red.
Yes I should have been more clear, the only setting I touched on the view filter is the Projection/Surface Pattern Overrride. And thanks for welcoming me to the forum, been a long-time lurker.