"Some places like Matasano, Stripe, Github and I’m sure many others are aware of this and are equally aware that it has the potential to harm their company a great deal." I actually had the pleasure interviewing with Matasano. I thought their process was fun and really enlightening in regards to what they do. Everyone I met during the process were really cool (and extremely smart).
Honestly, there were none. I think giving someone a challenge to do a their own pace was a perfect idea. I interview candidates in a discussion format so I can attempt to gauge passion, competency, and potential. I have been interviewed by startups where the guy on the other end of the phone seems annoyed to even have the call. The fact someone in your position in the company does direct phone calls to engage your candidates is EXTREMELY positive because you are showing care for your company by being that involved to know your candidate.
Heading out to Mountain View for an on-site interview with Matasano next week. So far the process has been great for me too. It has been challenging but they (tptacek and co.) still manage to do a great job of moving things along quickly.
Hopefully I don't scare them off after they've flown me out (and I've spent 16 hours on planes and in airports).