Some remarks on how we measure.
I heard that if we have a proton, then it does not have a definite position until we measure it.
Imagine you're behind a wall, I can't see you. I have a basketball and I've written down the angle and speed of the ball. I do my calculations well, calculate the gravitational field, maybe the drag, the humidity, ..., I throw ball on ball. You, not very patient, start dancing around the point you choose for our experiment.
One minute I was hitting you with the ball. You scream. In that moment, my ignorance (nonknowledge) of where you are, collapses, and I know your position. More or less, because I hit you in the head, my calculations are wrong. I've calculated, you're a little behind the point you reached. If I hit you on the feet, my calculated point is too close to mine.
I think you got it. Every measuring instrument has its uncertainty.
The smallest things we can measure a proton are what? Electrons? Photons? Another proton? You chose the proton and got Anna's answer.
Think of a laser trap or optical tweezers. Photons have a pulse and laser beams, better together with an electric field, could theoretically keep a proton in equilibrium around a certain point. Perhaps it will be possible to disturb the system and calculate the position of the proton better than with any other method.
And then what? There will be a next check of Heisenberg's uncertainty principle.
You know the resolution of microscopes has gone beyond what was previously claimed? There is a wonderful article "Light microscopy below the Abbe limit", unfortunately in German and even without abstracts in English.
But your thinking is good. If you don't measure the proton directly, but within a system of dependent particles, you could disturb the system and take measurements of the whole system and then deduce the constituents.