If that's a problem for you (it is for me), then you can include those variables by launching the application indirectly, from a script which parses the environment.plist before invoking the application. Save the script below to a file called LaunchWithToplevelEnvironment.sh (or whatever you like) in ~/Library/LaunchAgents, then make that script executable (chmod a+x script_name): You use it by creating or amending the KeepAlive launchd plist file so that it has a two-argument ProgramArguments element: Remember to adjust the paths and filenames as appropriate.
[robg adds: I haven't tested this one.]

