Inspired by the ability of super-resolved fluorescence microscopy to circumvent the diffraction barrier, two-color super-resolution interference lithography exploits nonequilibrium kinetics in materials to achieve large-area nanopatterning while using visible light. Periodic patterns with super-resolved features down to tens of nanometers have been demonstrated in thin films and monolayers. Extending these advances to the bulk nanopatterning of thick films requires a quantitative understanding of the time-dependent interactions of optical dynamics, including absorption, diffraction, and intensity modulation at two wavelengths, with the photoactivated and inhibited reaction kinetics. Here, we develop an efficient electromagnetic (EM) perturbation theory approach that facilitates for the first time fully coupled simulations of EM and chemical kinetics in two-color interference lithography. Applied to a spirothiopyran-functionalized photoresist system, these simulations show that diffraction and absorption effects are negligible (<0.1%) for depths up to 10 mu m, and that tuning exposure time and intensities can lead to concentration contrast up to 80%. We investigate multiple exposure strategies to reduce the pitch of the line pattern including sequential exposures with different times to achieve uniform lines and multiplexed exposures with equal periods. This capability to rapidly and accurately predict the coupled optical and chemical dynamics facilitates the computational design of high-precision patterns in two-color interference lithography.