Question?
If the jet stream is moving faster than the speed of sound, will the airplane experience the boom when breaking the sound barrier?
My gut tells me NO. They are moving with the air mass, not ground speed.
Although the speed of sound is lower at high altitude, they mostly fly in the Mach .80-.86 range, depending on the aircraft....which means they are flying at 80%-86% of the speed of sound regardless of their groundspeed.
You have to exceed Mach 1 (actually about Mach 1.1 to get a sonic boom).
You are correct about the jet’s speed moving in the airmass. The only commercial jet than can exceed the speed of sound was the Concorde.