I answered some of this in earlier posts, but here goes:
The J2EE version is optimized for performance and runs faster than the Standalone version.
According to Macromedia, the performance difference is most significant on larger installations with multiple CPUs.
Based on my experience with the CFMX Standalone server used in the port, and the CFMX for J2EE in the beta -- they, indead are separate products. There are differences in the way the are deployed (directory tree), and there are different options for clustering, and other advanced options. For example, with CFMX for J2EE under JRun it is trivial to setup duplicate CFMX servers and cluster them and attain automatic load-balancing.
The CFMX for J2EE contains all the bits necessary to run Web Services
The JRun for Mac OS X product allows you to connect [a CFMX server or a cluster] to the OS X Apache web server. If you connect to Apache, your CFMX URLs don't need a port number -- just the CFMX context root. For example:
So, your cfm, JSP, PHP, HTML can all share the same web server -- nice!
I only use the port when I need to do something for the articles -- I much prefer the J2EE product, and I think that you will too.
Strategicly, this is good for Apple and Macromedia -- Apple gets a J2EE-certified app server with Jrun.
Macromedia gets a entry (for CFMX developers) on the OS X platform.
I suspect, that if /when Macromedia releases a production product for the Mac it will be CFMX for J2EE.
If this happens, the Xserve/JRun/CFMX for J2EE combination should compare pretty well to the offerings from other major vendors of enterprise solutions.