Most probably, neither RE or RM are able to automatically detect the nature of the rig. So everything is currently left to the a correct tagging from the profiles author.
The thing must be rethought I believe, with a special flag written in the files themselves (both amp and cab) when they are created on the Profiler.
I wondered this... But I'd be surprised if the KPA team didn't put a flag in the profile somewhere to tag it as merged, much like they must have done to mark a bass rig. For us 'real' cab guys who have the power head or a separate power amp the merged profiles were somewhat of a revelation. Cab driver did an amazingly good job most of the time, but now merged profiles are out there I only use merged or DI, they are just so much better. If there really isnt a merged flag in the profiles then it is a bad oversight because even if a flag was added now it's a bit late - a lot of the commercial profilers have invested a lot of time and effort adopting merged profiling and for those profiles to miss being included in the results if such a filter was added in the future is simply unfair.