When you use eclipse.exe then eclipse.ini file is used rather than ccstudio.ini. That is what causes your default workspace to be different. You can compare two files in a text editor to see that ccstudio.ini defines default workspace path differently. I think you should be able to just use eclipse.exe switch to your other workspace and then use that as eclipse remembers your last used workspace... i.e. I am not sure that I would suggest overriding that variable). It is useful for when someone wants to have multiple desktop icons each associated with a different workspace. However, if it is just one, then I am sure what the benefit would be. There are some other settings in ccstudio.ini file that may or may not impact you. The intention behind keeping eclipse.exe is to allow end users to have a stock eclipse user experience without TI's customizations.
Martin