E = m c^2
was checked before in hundreds of different totally different experiments, with completely different sorts of energy variations.

If these calculations, that seem to use Quantum Chromo-Dynamics on a space time grid, come out with the right mass, it does say much more about

• the correctness of the QCD theory
  
• the accuracy of the approximation made, by discretising the space time, which, even if it may be discrete for sure isn't to the used dimension.