I think the OP is right in his questionings and probably a lot of students are shortchanged by not having these things explained properly.
The expansion of liquids with temperature is a complex phenomenon for which the theory is unlikely to be complete. There might be a rough theory to suggest why roughly most liquids would increase in volume roughly proportionally to another. But I am sure no two liquids would expand exactly proportionately to each other. When they invented the mercury thermometer there was not even a glimmering of a theory. But mercury would be more convenient than others, and you might think the temperature measured by the length of a mercury thread might mean something even if you didn't know what. BTW you don't need to use length of liquid columns - many physical measurements might do, e,g, electrical resistance of some substance or other. But if you didn't have a physical understanding what use was it?
At first standardisation and discrimination. Early scientists had only a qualitative description of temperature - terms like 'dung heat' or 'furnace heat'. There were only at most half a dozen different temperatures! Even without a theory it is quite useful to be told that a chemical reaction goes well between 60 and 89 deg. And for the human body just a few degrees turn out very important for health and disease and diagnosis, so an instrument to measure within a fraction of a degree instead of judging the degree of fever is very useful.
(In one way on the other hand temperature measurement was ahead of others. All measurements are comparisons. When you report a measurement in units you are comparing something with something else in some other laboratory where the instrument was directly or indirectly calibrated against some standard. A meter and a gram were originally blocks of stuff in some laboratory in Paris. But for temperature you could make your own standard where you were agreeing with others because the freezing and boiling points of water are the same everywhere (simplifying). These days they try to get standards like this that can be reproduced everywhere. When last I heard they had got this for time and length but not yet mass.)
Then came along the kinetic theory of gasses and their volume at constant pressure was proportional to the average kinetic energy of the molecules so this volume resembled the mercury thermometer but reflected something fundamental and understandable. So That could be the measure of temperature. Well, you still need a substance that is near enough to what the theory is. OK - dilute noble gases. I remember that there was a gas thermometer made of platinum filled with argon in some standards laboratory somewhere. So all decent thermometers were calibrated, no doubt mostly indirectly against this. You cannot check experimentally that the volume of this argon is linear with temperature of course - that would be circular. But you can check experimentally that other predictions of the theory like Boyle's law are well obeyed.
So through this chain of comparisons we are able, maybe without thinking about it, to measure e.g. rates of a chemical reaction, varying with our temperature measured with our (ultimately calibrated) and explain the dependency quantitatively in terms of an activation energy because we know an energy is essentially what our thermometer is reporting to us.