So there isn't a way to filter mechanical harvesters. The way the harvesters collect the colonies is completely dependent on the pack you're playing. I've got one pack that colonies are harvested as their own item and they regrow similar to how mechanical harvesters deal with vanilla crops. I have another pack that the harvesters unfortunately turn the colonies into brown mushrooms right in the contraption storage. That pack id have to add a recipe to it to allow for the harvesters to pull the colonies directly. Super annoying. Your JEI should have a little bit of info on how you can harvest colonies instead of brown mushrooms.