In the majority of cases of people buying MC, this doesn't happen. Why? Because most people don't buy MC without first trying it. So, they first download the free, fully functional, 30 day trial, install that, and test it out. Later, once they decide they want to pay for it, or the trial runs out, they buy and get the MJR file. Installing the MJR is easy because JRiver MC is already installed at that point.
I do agree that this is a slightly confusing point about MC. But for the majority of MC customers, it doesn't appear to be an issue.
I'm glad you got your copy licensed and running. If you have other questions about operation, please post here and we'll try to help you out.
Brian.