Yes every theory is just a model to fit observations etc etc. But Atoms are conceivable - they work as a model, but we can also imagine how to fit into the reality that we experience. We can 'see' them to an extent with special instruments. And their abilities/behaviours are evident in all the physical world of compounds and elements around us. You can disolve salt in water, you can light up a neon sign.
Quantum Mechanics is a model that fits experiment results very well, but is very hard to conceive of. Wave function collapse has no obvious analogue in the world as we experience it. Thats the point of schrodingers cat. You either have to go for the many worlds interpretation, or get into spooky stuff about observers.
Spacetime/relativity is similar, we can do stuff like fly a clock around the world in an airplane, or observe mercury transitioning past the sun, but its much less conceivable based on our everyday world. So spacetime might just be a constuct, like wave function collapse, that doesnt map easily onto our experience of the world. Certainly its a question worth asking.