No noise when one volume pot zeroed with both pickups is standard with that wiring arrangement. It's what I'd call 'Gibson' wiring and all twin pickup Les Pauls, SGs, Flying Vs etc. have the same issue. One reason there's a pickup selector switch! for when you only want one pickup on! I think the Rickenbacker wiring method prevents this, but it is more complicated circuit and needs a different type of selector switch.

The 'both pickups on' volume issue is down to phase cancellation, and lowering the output of one pickup reduces the cancellation, actually making the output louder in this instance! If the pickups were fitted in slightly different locations on the body, you'd get another set of output interactions which may result in a thinner and quieter, or louder and thicker, mixed sound. And changing the pickups for ones with different tones is also going to give a different mixed position sound.

If it really bothers you, then I'd suggest playing through a compressor, set with just enough compression to help balance the levels.