I asked IDM Support this question, independently, a while back. I trust that the etiquette here allows me to post their response?
We are aware that UE3 will not launch UC3 Professional, but unfortunately this is unavoidable.
Essentially, there is a technical restriction that prevents UltraEdit (or any application for that matter)
from launching a separate U3 application from the U3 drive. Therefore, in order to use UC3 Pro, you
would need to launch it separately and perform your compare/merge operations through UC3 Pro
Please understand, this is not an UltraEdit limitation, rather it is a technical limitation for U3. If the
technology allowed it, we would certainly do our part to address it in a timely manner. However,
being that this is a limitation with the U3 system itself, I don't know whether Sandisk/etc will add
support for this functionality on their U3 system.
Even though U3 has a technical limitation, our engineering staff is still looking at a future merge of
the two applications as a potential solution. In this case, UE3/UC3 would essentially be one
application and resolve the current U3 restriction.
I just wanted you to know that we aren't accepting the limitation and have a long term strategy that
solves the issue.