Eating chocolate is associated with improved brain function

Absolutely correct.

So that can't be how scientists operate

I'm torn between writing "citation needed" and "unwarranted conclusion from stated premises" so I'll go with both.

The head of the department where I did my physics undergrad spent years, decades, measuring everything there was to measure about plasma: Energy input, energy output, temperature of the phase change (plasma is a distinct phase of matter), spectral distribution, etc., etc., etc.

He wrote many papers, primarily on his measurements, and also on how he refined and improved the measurement process. I don't recall at all well, but I don't believe there were overmany hypotheses, let alone theories. He was about data, not models.

There are theorists who spend the bulk of their time with pens and imagination, occasionally - for some, rarely - checking in with the empirically real world.

A very few of these have names we celebrate for changing the shape of the world - Darwin, Newton, Einstein. And these particular luminaries knew the shape of the real world, knew existing theory didn't fit. (Newton is famous for saying he stood on the shoulders giants. Kepler was one such. Kepler measured and measured and measured and devised a relation. No theory, just a relation to link his measurements.)

Without the many scientists who do nothing but measure, measure, measure, scientists many of us would consider tedious drudges, these luminaries could never have known that theory didn't fit data. Or that data didn't fit intuition. Or that data was just plain weird.

Science does indeed proceed this way, bottom up, from measuring anything and everything of interest (to someone - maybe not to most of us, but to someone - I invite you to read The Map that Changed the World).

Science also proceeds from the top down, from theory to measurement. But often because there was another theory that failed to align with existing measurement. Think general relativity and its better prediction of the motion of Mercury, which failed to align with Newtonian Gravitation, which itself would never have arisen had Kepler not spent so many hours measuring, measuring, measuring. (And general relativity was a generalization of special relativity, which was created to explain a particular vexing measurement, the constancy of C. Einstein did not set out to reinvent gravity, he started simply explaining how C might be constant. He got to gravitation when he generalized relativity to non-inertial reference frames (that's what the special meant: inertial reference frames only).

We measure first. Just because we are that curious.