Heterogeneous systems-on-chip (SoCs) increasingly rely on domain-specific hardware accelerators (HAs) to deliver performance and energy efficiency gains beyond what general-purpose processors can provide. However, operating systems (O/S), such as Linux, assume that processors are the Compute Elements (CEs) and HAs are peripheral devices rather than specialized CEs. As a result, HA execution incurs substantial software (SW) overheads that reduce the effective benefits of hardware (HW) acceleration. This work demonstrates that significant inefficiencies arise from ``O/S peripheral device taxes'' (O/S taxes), including SW stack-accelerator communication, invocation, interrupt handling, and scheduling. We built MEERKAT, a Field-Programmable Gate Array (FPGA)-based framework for configurable multicore systems that include HAs; it allows the user to migrate Linux O/S support from SW to HW and identify, study, and quantify the impact. Here we study four major sources of O/S tax and introduce techniques to mitigate them. These include a virtual-memory-aware (VMA) communication method that enables efficient HA access to application data, a lightweight HA invocation interface, Interrupt Policy Adaptation (IPA) for dynamic polling and interrupt selection, and an HA-aware scheduler that dynamically distributes work across Central Processing Units (CPUs) and multiple HA instances. Experimental results demonstrate up to $260\times$ faster communication and $2$--$6\times$ performance improvements in wall-clock time over conventional schedulers. Furthermore, our study reveals that overall system performance depends not only on HA speed, but also on O/S overheads, resource availability, and scheduling decisions. These findings highlight the importance of treating HAs as first-class computational resources and motivate a more accelerator-centric O/S design for future heterogeneous systems.

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