Precise control of composition and internal structure is essential for a variety of novel technological applications which require highly tailored binary quantum dots (QDs) with predictable optoelectronic and mechanical properties. The delicate balancing act between incoming flux and substrate temperature required for the growth of compositionally graded (Si1-xC x; x varies throughout the internal structure), core-multishell (discrete shells of Si and C or combinations thereof) and selected composition (x set) QDs on low-temperature plasma/ion-flux-exposed Si(100) surfaces is investigated via a hybrid numerical simulation. Incident Si and C ions lead to localized substrate heating and a reduction in surface diffusion activation energy. It is shown that by incorporating ions in the influx, a steady-state composition is reached more quickly (for selected composition QDs) and the composition gradient of a Si1-xCx QD may be fine tuned; additionally (with other deposition conditions remaining the same), larger QDs are obtained on average. It is suggested that ionizing a portion of the influx is another way to control the average size of the QDs, and ultimately, their internal structure. Advantages that can be gained by utilizing plasma/ion-related controls to facilitate the growth of highly tailored, compositionally controlled quantum dots are discussed as well.