Well, the problem now is that in the proposed new theories clocks also can exhibit differences in their readings if working at differences velcities but because the proposed electric and magnetic fields (which also governs atomic scale phenomena) have a new factor in their definitions which is velocity dependent.
If you are talking about SR time dilation then you need no such factors. Electromagnetism, as Maxwell finally formulated it, already predicts that moving systems held together by electromagnetic interactions will experience time dilation (and length contraction, for that matter). This was noticed by the likes of Lorentz and Larmor in the last years of the 19[sup]th[/sup] century, several years before Einstein's 1905 paper.
The whole point of relativity is that we know what the time dilation factor will be from a symmetry argument, because electromagnetism is a relativistic theory,
without having to do detailed electromagnetism calculations like Lorentz and Larmor originally did.
That said, the dominant effect reported for the GPS satellite was due to gravitational time dilation, which is dependent on altitude and the gravitational field, and not on velocity.
Then, as a possible new interpretation is possible to explain the timing variation it cannot be considered a proof anymore.
Your choice of language is strange because there is no such thing as a "proof" of anything in experimental physics. The scientific method implicitly recognises that just because a theory makes a correct prediction doesn't necessarily imply it is the
only possible explanation of the result. So an experimental result is never a proof and that is not how we use evidence in science.
The way we use evidence in science is different: if a theory predicts result A, and the foundation of the theory is small and has nothing specifically to do with A, scientific policy is not to regard that as a coincidence. By making
lots of measurements, we expect to filter out the right theory.
The reason we think general relativity is a "good" theory is not just because it manages to get the right results, but because it is a theory that depends on just two parameters (the gravitational constant
G and the speed of light
c, both of which were fixed beforehand), and the theory didn't need to be fiddled around with to get the right results. The bending of starlight is considered strong evidence for GR partly because it was observed
after GR made the prediction. The same is true of gravitational time dilation and the rate of GPS satellite clocks: GR was formulated in 1915 and made correct predictions about experiments performed decades later, without any need for "interpretation". So when you say that other explanations might be possible, you are technically correct, but you are missing the point and not addressing why we consider these results good evidence for GR in the first place.
By the way, there, in Appendix B, is presented other interpretations possible for Mercury's precession and the bending of light by massive objects like the Sun.
Other interpretations for other phenomena and experiments are even described within the text.
Then many considered experimental tests in favor of Relativity could not be considered totally valid evidence in favor of Relativity only anymore. They are also compatible with the new theory.
I think the appendix you refer to is a perfect example of what's wrong with your approach to physics: you need to make up a new explanation for every effect you consider, and you never show that you can get the right numerical result. Regarding your attempt to explain Mercury's perihelion advance, I think it also doesn't help you that 19[sup]th[/sup] century astrophysicists weren't stupid, and if they knew how to account for perturbations of Mercury's orbit due to the other planets, they could certainly have dealt with an asymmetry in the mass distribution in the sun if they had expected that to be significant. It also doesn't help you that the sun is quite well studied and if there were a significant asymmetry in its matter distribution, I would expect we would know about it. You are doing nothing to establish that what you are saying is significant, hasn't been considered[sup]*[/sup], and is actually consistent with what is known about the sun.
[sup]*[/sup] a
quick check at Wikipedia reveals that at least the oblateness of the sun, leading to a quadrupole moment in its mass distribution, was considered and accounts for 0.0254 arc seconds per century of Mercury's perihelion advance. Astronomers apparently also tried explaining the perihelion advance in terms of another as yet undiscovered planet, and had fun predicting where that planet might be.