The OS of the MX-3000 is not updated by the editor. The OS is embedded in the remote. The firmware is updated with the editor software which is really what is most important.
Windows CE runs applications, in this case only one application, the firmware. When firmware is updated it is like getting a new version of Word or Excel that supports new features. Think of the .rcc file created by the editor software as a word or excel file that is loaded by the application.
The version of the OS is of limited importance, but not a major concern in most cases.
There are 10 types of people in this world, There are those who understand binary, and those who don't!