A better practice is to use the application "A Better Finder Rename" to change the name of the new file.

http://www.publicspace.net/ABetterFinderRename/

I have been using this application since I started using Catalyst at it's beginning. I have about a dozen settings that I either enable to disable to change the file names and their extensions.

Oh and FYI, the file conversion that Catalyst does is actually being done by the Quicktime Framework at the core of the OS X Operating System. Catalyst is just running a tool which calls these services to perform the conversion.

The renaming of the files is a tool so that Catalyst Users can recognize different files.