But EM laws do break down at the atomic level, which is why we have quantum theory. So the question is not whether they break down. The question is: at what point are they no longer valid?
At this stage I am cross-examining the evidence. I don't have to come up with a valid theory at this stage to test the prosecution's case.
In an ideal world I would have read and understood text books on quantum theory, tensor analysis, and general relativity and know how to develop Schrodinger's equation from first principles. I don't live in an ideal world.
But IF <A=the existence of the strong nuclear force> is in some part based on the assumption that <B=the EM field equations apply down to the surface of the proton>, and IF <C=EM field equations are known to break down at some point at the atomic level> THEN the onus would be on the proponent of A to show B is true. I don't have to lead evidence for a verdict of 'not proven'.