That's true. However, unless I'm mistaken (my field is more chemistry-simulation than physics-simulation), the internal nature of the proton is not necessary for achieving chemical accuracy level results from something like FCIQMC, namely because the chemical properties of interest are the result of only the charge interactions of the protons/electrons as potential terms in the Schrodinger equation. I believe applying QMC to solve that equation for all charge-charge interactions (including electron correlation) is enough to reach essentially exact energy levels (in the limit of simulation time -> infinity) ... am I incorrect? I mean, there's probably some difference in the eleventh decimal place due to the lack of relativistic and radiative corrections.
Sure, just wanted to point out how complicated truly "simulating reality" is. :)
I mean, my doctorate involved calculating tiny, tiny corrections (8 or 9 decimal places) to hydrogen-like energy levels, but even there I could still treat the proton as point like!
Hmm. I need to research this some more.