This study presents a control-oriented strategy for enabling safe and efficient operation of a dual-mode RCCI–diesel research engine using a stock single-stage turbocharger. To the authors’ knowledge, the specific challenge of controlling charge-air pressure in a heavy-duty cyclops RCCI–diesel configuration, where one RCCI cylinder and three conventional diesel cylinders share the same stock twin-scroll turbocharger, has not been experimentally addressed in previous RCCI boosting studies. The originality of this work lies in using cylinder-individual combustion control to regulate scroll-wise exhaust energy distribution and turbocharger operation without external boosting hardware or major airpath modification. Conventional low-temperature combustion (LTC) engines often require costly external supercharging systems for sufficient charge air supply, but the proposed approach combines stock turbocharger hardware with a real-time control algorithm to extend the operable load range. Four complementary strategies – advanced start of injection, increased rail pressure, selective activation of the RCCI cylinder and rebalanced diesel injection quantities across cylinders – were coordinated to regulate exhaust thermal load on the twin-scroll turbine. Steady-state experiments at >200 operating points demonstrated successful control of turbocharger operation within surge, choke and thermal limits, while supporting the RCCI cylinder’s pressure-ratio demand between 1.0:1 and 3.48:1. The developed algorithm enabled stable engine operation up to 686 kW, with peak turbine inlet temperature constrained to 597 ◦C, below the 600 ◦C material threshold. Sensitivity analysis revealed that engine load was the dominant driver of turbineexhaust temperature (42.9% upper case, 27.4% lower case), whereas injection timing and rail pressure provided negative sensitivities, confirming their thermal mitigation role. RCCI cylinder activation and diesel rebalancing strategies effectively redistributed thermal load between turbine scrolls, offering robust scroll-wise management of exhaust asymmetry. The findings highlight a low-cost, software-driven pathway to extend the operability of RCCI engines without hardware modifications, demonstrating practical relevance for marine and large-bore applications. The methodology contributes to the advancement of sustainable, high-efficiency combustion concepts by integrating conventional boosting components with advanced combustion control.