Quantum dots are semiconductor nanocrystals that absorb and emit light at wavelengths tunable by the size of the crystal. Size-tuning provides access to a broad range of optical spectra, however it is fundamentally problematic for many applications because it leads to a large mismatch in absorption cross-section and fluorescence brightness across a series of colors. We have recently demonstrated engineering strategies to generate multicolor, extinction-matched, and brightness-matched quantum dots based on colloidal multi-domain core/shell structures. We use alloyed cores with composition-tunable bandgaps and finely adjust the domain size and electronic properties of the shell to precisely match both absorption cross-section and quantum yield. Using this strategy, it is possible to tune fluorescence wavelength, extinction, and quantum yield independently, vastly expanding the photophysical landscape of these materials. Moreover compared with conventional size-tuning strategies, this enables access to a wider spectral range with compact dimensions. The equalized optical properties translate from the ensemble level down to the single-molecule level, setting the stage for new possibilities in highly quantitative, multiplexed imaging in cells and tissue. However selection of appropriate structural parameters to generate specific optical properties is challenging without insight into the photophysics of these materials. Here we describe the evolution of the optical properties of alloyed cores during the shell growth process that provide new insights into general engineering strategies.