Starting from v1.2.6 (released April 13, 2015), mono is not required to be installed.
The game contains standalone Mono bundle to run the game server.
To run the game server without the Mono, you should execute (on a 32-bit Linux):
It's fully native executable, which contains statically linked Mono with all required dependencies and which will use classes from "VoidExpanse.ServerMono.exe".
If you still want to run the game with Mono installed into your OS (be sure you have complete Mono 3+ installation), you could run it as previous:
The "VoidExpanse.ServerMono.Bootstrapper.exe' is added only for compliance with Mono LGPL license, to allow the user manually build a bundle with any version of Mono.
The singleplayer mode is always using bundle executable (if you not remove it, otherwise it fallback to Mono in OS).
For hosting multiple multiplayer servers it's better to use Mono installed into your OS - it will use less memory for Mono runtime as it uses dynamic libraries.