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For me it was a combination of both a blown speaker and the assembly going bad on the passenger side. The dealer had to replace both to completely resolve the issue. I wonder if the assembly going bad contributes to movement in the speaker which causes it to blow more easily. It sounded terrible, and doubly so if the windows or sunroof were open... I guess the lack of pressure allowed the woofer cone to extrude further which made it sound worse.
It is the speaker assembly itself. The “rattle” sounds more like a blown speaker. Your symptoms are early onset of it.
Cars are meant to be taken apart and serviceable. No great shakes. Given how much of a modern car simply snaps together, I keep a bunch of replacement clips on hand.
Where did you source the replacement clips?
Also, when you say the speaker assembly itself, meaning the entire speaker has to be replaced and placing material (dynamat, etc) on the interior of the door won't fix it?
I only notice it on my driver side door, when playing really, really bass heavy music, which I only really do when my son is in the car.
I agree with OP's assessment that Bose is definitely better than the base system I have in my T. Even the loaner Cayman I have currently with a Bose system sounds infinitely better than my car's system. Here's a pic of the sub in the spare tire compartment, kinda cheesy looking but still sounds good. I wonder how hard/expensive it would be to get my car's stereo upgraded to a Bose 992 specific set up?