Possible to ignore certain pieces of features?

Is there any way currently to tell features to ignore a certain piece of an included component? For example, I have a base feature we use to take a vanilla site to a configured site for a group of sites we manage. We use the pathologic filter to correct inline filter URLs between our development and production sites. However, because each site has a different configuration for pathologic depending on the site URL, Features always returns that the feature is "overridden." Is there any way to tell it to ignore pathologic settings on the input filter? Any pointers in the right direction would be appreciated!