Two-tier championship would make sense if all participants in class A were faster than in class B. Which happens in WEC, or WRC and their subclasses. In 1987, when the "normally aspirated" championship was created in F1, those teams could barely make it into the points without attrition races.
But as of now, both Force India and Williams are ahead of both Renault and McLaren-Honda in the championship. And Red Bull is competing with Mercedes and Ferrari for race victories. While you could argue works team might have a little bit advantage over a customer, there is no distinct class A or class B in the overall results. If anything, having a more powerful engine is a greater differential, i.e it is better having a customer Merc than a works Honda. Maybe Honda should be in their own class B at the back of the field. 
Agreed, sportscars and rallying the lower classes actually run to clear different sets of technical regulations meaning there will always be performance gaps as a result. Similar thing in 1987 F1, two clearly defined separate engine regulations. The Clark and Chapman cups were actually scrapped for the last year of mixed turbos and NAs in 1988, because the idea that restricting the turbos even more was meant to be more of an equivalence formula, even if it didn't work out fully that way in practice (it hardly ever does).
In modern F1 everyone runs to the same technical regulations, some teams have more resources and/or better situations in terms of good in-house engine development, or are just plain better and will do a better job but that's not a multi-tier thing, and it's always been the case. Never mind different engine modes, Manor, TR and Sauber running year old Ferraris was rare to the point of noteworthy in the past 3 years, in the past it was the norm customer teams would get a 1 or even 2 or 3 year old engine based on what they could afford. Even when 90% of the teams ran DFVs the bigger teams often had access to better tuners, or smaller teams would be running older tired motors with more miles on them. The HP gaps were probably smaller but they were always there.
Plus while not necessarily relevant when talking about the present moment only, the pecking order can be very fluid over time. If someone had said around 2002/3 that the Jaguar and BAR organisations would sweep all titles between 2009-2017, and that from 2005-17 that Williams and the Minardi organisation would win the same number of races as each other, they'd have been carried off to the nearest padded cell.
