At a small company with specific goals, there's no implication of doing "'science' in general". I can buy that the idea of being chief scientist at, say, IBM or Google or Microsoft is a little fluffy, but if you're a startup focusing on one goal that is a little beyond what the scientific community knows how to do in theory, it's entirely reasonable to have a position in charge of guiding and directing (and performing) research to that goal and keeping up with the state of the field.
It's largely equivalent to a PI role of a university research project, except that there are things going on in the company other than pure research and so there are chief officers of other things too. Nobody thinks that "primary investigator" is a fluffy title on the grounds that people don't do investigation in general; it's clear they're investigating specific things.
You say "Nobody does 'science' in general", but you are wrong. Many people work at organizations that have a broad range of scientific pursuits in a broad range of fields of study. The Chief Scientist's job is "ensuring that [the organization's] research programs are widely regarded as scientifically and technologically well founded and are appropriate for their intended applications".
Dude, Amgen and a ton of other biotech/pharma firms have "Chief Scientists" or "Chief Scientific Officers" on staff. Sure, they work in specific fields or specific departments, but that is absolutely a valid and commonly used title.
