When you say ab initio calculations, could you cite the level of theory? I think there could be some ambiguity given differences in scope.
Other people use ab initio very differently (for example, since you said "level of theory" I think you mean basis set). I don't think something like QM levels of theory provide a great deal of value on top of classical (and at a significant computational cost), but I do like 6-31g* as a simple set.
Other people use ab initio very differently. For example, CASP, the protein structure prediction, uses ab initio very loosely to me: "some level of classicial force field, not using any explicit constraints derived from homology or fragment similarity" which typically involves a really simplified or parameterized function (ROSETTA).
Personally I don't think atomistic simulations of cells really provide a lot of extra value for the detail. I would isntead treat cell objects as centroids with mass and "agent properties" ("sticks to this other type of protein for ~1 microsecond"). A single ribosome is a single entity, even if in reality it's made up of 100 proteins and RNAs, and the cell membrane is modelled as a stretchy sheet enclosing an incompressible liquid.
I also agree that QM doesn't provide much for the cost at this scale, I just wish the term ab initio would be left to QM folks, as everything else is largely just the parameterization you mentioned.
I am more than happy to use "ab initio" purely for QM, but unfortunately the term is used widely in protein folding and structure prediction. I've talked exdtensively with David Baker and John Moulton to get them to stop, but they won't.
In inorganic materials ab initio means you actually solve Schrodinger's equation (though obviously with aggressive simplifications e.g. Hartree-Fock).
Having developed a few newtonian force fields, calling them "derived from QM" is very, very generous :P