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Given the 9 panes of glass the Model Y has, I'm not surprised that simply replacing the two side panes makes no difference to sound levels. Looks like the lamination is primarily for shattering safety (unless you drive into a lake and need to break free).
I would check with a different SC. Earlier there was a post (on Reddit) that the front seat tempered glass windows could be replaced with the newer laminated glass windows by Tesla for ~$1300 US.
It looks like there is more to it than just swapping the glass. Take a look at this video and pause at the 1:17 mark. Notice how different the attachment area is.