I don't remember if this is desired behavior or not, but cc'ing @RHo and @MMiller_WMF to clarify. Basically, if the user does what we ask them to (click on the blue call to action button) they'll keep seeing the homepage welcome tour. In order for our code to update the preference marking the tour as completed, the user has to either deliberately click the X or click outside of the tour.
My proposal would be to mark the tour as completed in the user preference as soon as the user clicks the blue call to action.