Since you asked: I'm one of the principals at Fly.io. Before that, I was one of the founders of Latacora, which embeds directly inside of startups for years at a time running their security teams full time. Before that, I founded Matasano Security. Before that, I was a Product Manager at Arbor Networks, after being the lead developer on their DOS product for a couple years. I'll stop there (I'm older than the median HN commenter).
Later
For what it's worth, for companies literally chartered to do scientific exploration --- drug discovery chemistry, for example --- I completely buy that there is a real "Chief Scientist" role, though I can't claim to understand that role well enough to defend it. But that doesn't describe any software company anywhere. Regardless, "CTO" is something different.
What industry are you in? In deep-tech / hardware the role of chief engineer is well understood. In biotech it is sometimes called chief scientist.