This is an old subject but you could argue that the filter in the liner is there to protect against the liner overflow. And the filter at the suction controller is there to protect firstly the suction controller and then more importantly the pipeline.
E.G Most, if not all modern controllers will not operate without some sort of filter or float cut off attached. If a user connnects a drain to the controller direct (by passing the liner) the consequences of the secretions getting sucked up into the pipeline could result in both plant and pipeline failure or mass contamination of the pipeline.
Believe it or not some 20 odd years ago we used to flush vacuum pipelines and you would be shocked at what would come out at the plant end.
