You're right...that is the part that doesn't matter. But the kernel still has to coordinate and schedule that. The kernel has an inherent overhead for execution

You're right...that is the part that doesn't matter. But the kernel still has to coordinate and schedule that. The kernel has an inherent overhead for execution and context switching, and will always have some amount of code that is hot. The reason microkernels typically benchmark on syscall (typically IPC) latency is because that is the only truly apples to oranges part that you can't compare between the two. Monolithic kernels have a single context switch, microkernels have two. But microkernels, being micro, are a lot friendlier to caches (less to load and flush), and especially so with dedicated code caches (which do not need to flush on context switch).