Actually, I can tell you that the following facts are true:
1) Maestro and the corresponding mission software were developed almost entirely on workstations running Linux and other open source software
2) The official workstations that are running this software at JPL run Linux
3) Most of the testing and optimization was done on Linux, thus you can expect Maestro to run best on Linux
4) We distribute different installers just to make it easiest for people to get the correct versions of all the required components onto their systems (for example, with the exception of the OS X installer, I believe, all of the installers include a private JRE installation). The various installers are actually all automatically generated by scripts from the same codebase.
one of the SAP/Maestro developers (currently back at MIT)