I am so glad I found your blog this morning. Your situation was exactly the same situation I had. I have been running from one department to another and finally talked to somebody who has put some light on the situation.
First, what you are experiencing is a bug! Microsoft has a lot of cases where Marketing was installed on the production environment.
Second (and this is big, so you should sit down for this one). Marketing should be running on a parallel environment (not on your production environment). Consequently, you have a different contact and account database.
Steve Mordue's article is not clear on that point, so let's review the license: Marketing will count the number of contacts but it has its own database. You take the contact list from your production environment and import it in Marketing.
Finally, I was told by the technician on the phone that Marketing will be completely integrated with production by the end of this year.
I hope that helps you see better Marketing for Dynamics 365.