I have the exact same issue with my Bose QC headphones. Starting MSFS 2024 turns on the microphone in the headphones, which changes them into transparency/voice mode, and the audio sounds horrible.
I have not only disabled permission for MSFS 2024 to use a microphone, I have disabled the microphone in my Bose headphones in Windows system settings. That microphone shouldn’t even be an option for any application in Windows. Yet, when starting MSFS 2024, it still happens. Every time.
For what it is worth, I entered a ticket with Asobo. The ticket status has already been changed to solved. However, no appends were made to the ticket at all. I am hoping that simply means that Asobo has this fixed in a (hopefully soon-to-be released) update of the sim.