Well, in order to get results comparable to experiment, at some point the theory, whatever it is, needs to be converted back into the 3+1 dimensional space. Since this is where the electrons live. However, in principle it could be possible to perform the actual computations in a different manifold, and just obtain the 3+1 dimensional picture via a down-projection at the end, just before physical properties are calculated. Will this help? No idea. But it cannot be excluded.
I would recommend you to not argue with quantum gravity or high-dimensional space-times, however. In electronic structure, the goal is to obtain an accurate approximation of molecular properties arising from the (usually non-relativistic and time-independent) interacting Schrödinger equation. For all practical purposes, this is all the physical reality you need. The main question is: Can strange geometric theories be used as a viable tool for obtaining those approximations numerically? This is what you would have to find an approach for.
Note that geometric optimizations (e.g., transition state searches) use techniques of numerical optimization which are near 100% orthogonal to the techniques used for computing electronic structure (effectively, such geometric optimizations need only energies and gradients from the electronic structure calculations, and are more or less agnostic about the actual wave functions or electronic structure used.) To get into the electronic structure problem, you would probably best start with a method like Hartree-Fock, and see if you can find any way of making it "better" by using non-standard electronic manifolds (e.g., by making the orbitals, which are normally functions of one 3+1 dimensional coordinate (3 space, 1 spin dimension) functions of some other geometric manifold, and defining a way of down-projecting the obtained wave functions into 3+1 space for computing properties)