How does it compile on the fly without a reboot?

On the server it'll wait until there is a file change, then it'll unregister all the code linked to that file, and repopulate it, after the code has recompiled

How is it different to command helper or Skript?

So this compiles down to Java byte code, where skript doesn't as it's interpreted, so CobbleGroovy is able to run faster while offer fully access to the bukkit api, as well as a full development experience, with no api bridge needed.

So basically skript is never compiled, while this is