Would there be a way to filter the items the tower picks up? Be it a config option or an in-game gui that the player can set?

Interesting idea.
I have never learned/tried any script about filter (perhaps also a popup GUI to choose them), so I will need some time to investigate how to do it.

Just released 0.17.4, which allows using circuit network signals to filter/limit items to be collected. Hope it fits your request.
Please see FAQ for details and an example.

Just wanted to write back and say how awesome this is, this mod has made my life 1000x better, and the filter update is absolutely perfect