The shock waves from supersonic flight travel pretty much perpendicular to the direction of travel, so Peter is correct - during vertical flight the shock wave is unlikely to reach the ground. However to be useful, eventually they need to travel horizontally, and that shock wave will still reach the ground. They're quoting 100k ft. cruise altitude - the higher altitude means the shock won't be as strong when it hits the ground relative to something like Concorde, but will reach a wider area. Further, they're quoting 4.5 Mach cruise, which would make for a much stronger shock than Concorde's ~ 2.0 Mach. In short, I still doubt such a vehicle would be allowed to regularly cruise supersonic over populated areas.
I also question the value of the patent as anything more than a
PR exercise. First off, patent's expire, and we're talking an aircraft that is decades away. Further, much of the 'new' isn't so new. The Bomarc used a combination of rocket and Ramjet power 60 years ago, the XB-70 moved aerodynamic surfaces from horizontal to near vertical to improve cruise stability 50 years ago, the military has been using 'inward facing' seats since WW II, and while I'm unaware of anyone actually building an aircraft with a retracting engine, the concept is far from new. This stuff is public domain 'common knowledge' so even if a patent is granted, it won't stand up if someone challenges it.