Good points elsewhere, but I don't think these are actually assumptions.

Whether or not truth is accessible is an empirical matter that can be investigated; which phenomena are universally consistent can also be investigated; and so can what is and is not necessary for human flourishing on various timescales. It's just that the answers come back with such certainty--these days, though this wasn't always true in the past when we knew less--that is appears as if they are actually just assumptions. I mean, I assume I have two legs, also. Can I prove it's true, though?

I think you're on safer ground stating that scientists generally assume rather than document that the flourishing of humans is good. I don't think almost anyone is as blunt about it as Sam Harris; I don't think most people even think in those terms per se. Because everyone, scientist or not, tends to have that same viewpoint, at least these days. All else being equal, it's better to have flourishing humans than non-flourishing humans. One wonders, indeed, whether this isn't actually just a tautology smuggled into the definition of "flourishing".

Anyway, I don't think scientists are particularly different in this regard from anyone else. People in general want "their people" to do well, and in modern times we've managed to extend "our people" to more or less the entire human race, with scientists along for the ride. But the personal motivations are much more often because of curiosity and eagerness to know--or because they are good at it and can get paid for doing it, in industry--than magnanimous desire to enable humans to flourish.

Again, Sam Harris is a possible exception.

(Meanwhile, scientists have actually discovered that, actually, human flourishing is not our most fundamental goal, even if it's very often an effective proxy goal. However, despite the conclusion being essentially inescapable, people generally don't like to embrace this, especially not Sam Harris.)