I've noticed that that progress bar can sometimes be a bit misleading. What feature is before that implicit joint origin? My guess is that it might be something expensive, and the progress bar has incorrectly changed its display to the next feature.
To answer the specific question: An implicit joint origin is no different from a regular joint origin. That is just the name that is given to hidden joint origin that is created if you just pick geometry during the Joint command. Behind the scenes a joint origin is created. The compute of that should be fast. All it does is resolve the geometric reference.
To find out which features are expensive, in the text command window, type: "Fusion.DumpFeaturesByComputeTime". This will list out all the features, sorted by the amount of time it takes to compute that feature.
Jeff Strater
Engineering Director