If we rename the output jar, then it makes sense to also rename the output native libs. Those are overwritten as well when you do a compile_native_es. I haven't done that because Sys depends on the file name being lwjgl.dll/so/etc. Besides, if you need to build normal LWJGL locally, then you're developing something in the library, which means you know what you're doing and it's no big deal.
We should reconsider this in LWJGL 3.0 imho.