Mazda do not participate on the forum and are minimally responsive at the country level. My dealer knows of the problem and has a parts list for the fix. However he was unable to really explain what the root of the problem is and how the fix addresses it. I do not know if they have any documentation.
I believe that it is friction rubbing between the seal at the top of the door and the seal on the B pillar but I struggle to understand why opening the window affects it. When the car is in motion, perhaps the pressure change on the door moves it enough to affect the seal contact. There must be an interference fit rather than a pressure fit at some critical point and differences of 100ths of a mm are probably involved in explaing why one does or doesn't have the issue. (Note, most seals on a car body are rubber to paintwork and not rubber to rubber). It would appear logical that movement/clearance/rubbing is affected by temperature and I find that it is also affected by presence or absence of a passenger (passenger door is the issue).
The silicon spray solution works for me but I have to repeat it fortnightly so I have been experimenting with PTFE tape. After a couple of weeks I can get rid of 75% of the "rattle" with a single piece of tape stuck on the door rubber, but to eliminate the noise completely, one needs to cover around the edge curves. The outcome isn't pretty but it works and it isnt visible when the door is shut, of course: I may try to tidy it up a bit when I have the inclination. I couldn't find the tape in UK and bought it from China via ebay but it came quickly.
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