I've had a number of bikes that had chatter or pulsing in the disc setups. In all the cases it was one of a few things. First and most common was that the caliper was not pressing the pads to the rotor evenly. Mostly due to the caliper being something other than dead on parallel to the rotor. If the pads aren't pressed evenly they will scuff a little harder at each edge of each opening and make that chuffing sound you seem to be trying to describe. Some setups are reasonably tolerant. But I've had a couple which were hellishly sensitive to this issue. I had all these variations despite only dealing with half a dozen brands and models over the years.
The couple of times I had actual chatter which wasn't RPM related, just a wild operatic screech, it was some sort of contamination on the pads and thus on the rotor as well. Mostly from oily/greasy fingers in the shop but on one instance due to some oil I picked up off the road since the chatter started at mid ride after going through a small puddle on the road. Cleaning both rotor and pads fixed these in most cases. One time the pad had soaked the oil in so badly and cleaning was doing so little that I gave up and had to toss them.
The bottom line though is that vented rotors CAN run smoothly and quietly. But in some setups finding that setup can be a challenge to our fine tuning abilities.