Yes, for sure. In practice (and not at the 50,000 ft. level), you do try to include the multimodalities — you don't _really_ just use E[quantum_energy(r)]. But you ARE still reliant on some computable/smooth/Lipschitz moment and/or expectation from the quantum surface. The semi-heuristic argument for why you get away with this in biological simulation is somewhat heuristic, but of the following form:
- Most quantum field theories are described by of the form L(E), where E is an energy level ["effective field theory"] and the Lagragian changes as E change.
- When E is low, L(E) is classical mechanics & EM
- When E is around 1GeV, L(E) is the aforementioned plus QED
- When E is around 100GeV, L(E) has the aforementioned plus some QCD
- When E is at 1 TeV, L(E) has the aforementioned plus Higgs-like stuff
Now biology is on the lowest end of that scale, so you mainly have to deal with QED and perturbative electronic expansion. These electronic expansions are the most important part — you need them to get hydrogen bonding + electrodynamic molecular interactions correct — BUT they are highly local.
This locality is what you take advantage of when you normalize — you find from QM that the potentials only matter when the two charged/polar molecules are close, so you try to make a classical potential that has quantum 'jumps' when these things are close.
Do you miss the purely quantum stuff? Aharanov-Bohm, Chern classes, and the like? Of course. But from a practical standpoint, you do get the structures that you measure from experiment to be correct because the 'cool' quantum with 'tons' of states is less important for pedestrian things at low energy scale.
It is still hard to get right though! There's a lot of entropy you need to localize correctly and in some sense, you have to make sure you get the modes as a function of local particle positions correct.
The final thing to point out is that the Wick rotated path integral stuff works for biology much better than for real HEP-type of stuff because molecules are contained at low energies — those tunneling probabilities are O(h E), and log(E) is still dwarfed by -log(h) so you _can_ safely ignore them.
This is not true for things like circuits, however, because the lithography at EUV scales (3nm -_-) does have tunneling issues at high field strengths.
tl;dr: Biology has some saving graces that give you good approximations. Are they perfect? No, but if you find a time that I have to compute a vanishing first Chern class in a noisy, ugly biological system, then you deserve a Nobel Prize!