It also probably helps significantly that they could fly unmanned missions right away to make money while working out the bugs. You can't fly an uncertified aircraft for commercial purposes.
That's also the figure for just the Falcon-9 rocket. The Dragon cost another $800M. The engines were also developed in-house and may not be factored into that cost either (can't tell). So the total system is costing north of $1.1B.
The Boom model looks to be about the same size as a regional airliner, or a small narrowbody. For some recent points of comparison: the Bombardier CRJ1000 (developed 2007-2012) has a flyaway cost of $46M [1] and an estimated development cost of $300M [1]. A small narrowbody like the Bombardier Cseries costs $72-82M each and cost $5.4B to develop [3]. The Embraer E-jet E2 series (a second iteration on the E-jet airframe) is estimated to cost $1.7B [4].
It's much easier to develop iterations on a single airframe than to certify a new airframe from scratch. And those are all conventional construction, no carbon fiber or anything like that. And while you can develop components in-house - those need to be certified too. So much like any Not-Invented-Here syndrome - you really need to ask the question of whether you want to be a company who makes airplanes, or a company who makes airplane parts.
You can certainly do it some cheaper, but probably not a factor of 10. Overall I think Embraer tends to be one of the more budget-minded manufacturers.
[1] https://en.wikipedia.org/wiki/Bombardier_CRJ700_series
[2] https://www.flightglobal.com/news/articles/crj1000-takes-on-...
[3] https://en.wikipedia.org/wiki/Bombardier_CSeries
[4] http://www.aerospace-technology.com/projects/embraer-e-jet-e...