Yes, that's indeed a none-obvious issue, and looks rather strange on the graph.

That's not the 'partial evaluation' per se. Instead, it is the difference between RPython and HotSpot that surfaces here. RPython does currently generated singled threaded VMs, and neither the GC nor the compilation are done in separate threads. The HotSpot JVM however can do those things in parallel and additionally has other infrastructure threads running. In the end, this increases the likelihood that the OS reschedules the application thread, which becomes visible as jitter.