Just having a quick play around with it as had a thought that taking Premium tab out of the free version might have affected it.
You can test this altered version which includes the Premium tab in the free version .
My thinking is that simply changing the free version as having the premium activated already within it's own code, maybe making the free version still take precedence and hence why you still have the brand logo.
With having to physically install and activate the premium version as well, it might make the premium version overwrite the free settings and not display any mailpoet logo etc.
Not promising anything and I can already guess that this still might not work and it will have to still be masked out through code somewhere.
If it doesn't work then carry on with your current setup and include
@Kao X3 change to the mentioned php file and I will look to manipulate the code some day.

You should then get this in your licence window.
Then simply install the pro version from here and it will be good to go again.