Commercial requirements literally start at "one aircraft that gets the wings overstressed (if not actually snapped off) during destructive testing" and the requirements continue steeply onwards from there. You can figure on having it built by FAA-certified mechanics as well.
The FAA likes having a paper trail if the wings fall off (an extremely common problem with ultralight/sport aircraft built by non-certified personnel). Not OK when you're carrying passengers for hire.
I can completely see the expected extra cost of having to make two prototypes — and, yes, my first reaction to the article was: “please, please, let them have a billion in VC money”. But the truth is, the success ratio of projects about “we want to make a plane that goes that fast” seems far higher than success ratios of any company.
The business side sounds a lot more doable, given how many people fly those destinations and would like to do it faster.
I know several people (starting by my brother) who build their own plane (granted, it was a two-seater several several times louder than a grass-mower and seemingly slower, but you get the idea). One plane feels fairly doable as far as hard- to-predict financial issues go — if you have engineers who know super-sonic, and I can’t imagine having the idea without.