Hey -
Sorry for the delayed response. To answer your question about hooking P4V into the diff tool, I can say that yes it is possible. Inside Perforce, if you go to Edit->Preferences->Merge you can add your own custom merge tool for .uasset files. The following screenshot shows how to setup the parameters:
As for the problems with merging, I am still trying to find answers to what is happening. After speaking with other developers the middle “base” blueprint from the screenshot does not appear to be correct. We’re also looking into the error you receive when choosing the Accept Target / Accept Source option.