From what I've read the only thing that biopellets strip is nitrates, which I'm not sure is a bad thing, right? I don't think they strip anything else but I'm not sure about that. I'm running CoralVue BioSphere pellets btw, which I'm sure the type of pellets used can have a big impact.
If I want some dirt in my tank I can always reduce the amount of biopellets that are in the reactor and reduce its flow so not as much water goes through them. So far my tank still has algae that continues to grow on the glass and some buildup in the piping and hair algae still likes to grow in my refugium area (no more in the display though). Things are still getting settled though - I started adding a very small amount of biopellets several months ago and slowly increased the number to where I have about 1.5 cups for about 130 - 150 gallons of water. It's still a bit lower than what they normally recommend but I'm trying to keep from adding cyano or other uglies, which I got briefly the first couple weeks as things were starting to settle out.
My shipment of the "other methods" along with a test kit will be here next week. I will start dosing manually so that I can get a feel for how it impacts things, and when CA, Mg, Alk levels are where they need to be I'll send in a test. That's my plan anyways