Something like LuaJIT doesn't have the concept of a syscall, only calling into external C code. The same is probably(?¹) true for the JVM, since Java uses native methods to talk to the OS as well. So the JIT'ed code would call into the language runtime library, which in turn would call a syscall wrapper provided by the libc.

¹ It's possible the JVM, being the highly optimized workhorse VM it is, has specialized optimizations for I/O and does indeed skip over JNI and libc in these cases.