Wrong question: why shouldn't Google merge systems?
(as you say, there's no compelling reason for them not to)
Right question: Why did they release it in the current state, which is, I think it's fair to say, 1) a disaster and 2) technically rubbish for all the reasons in the OP.
You should be asking: Why, when building a cross-site system to leave comments, are their clever engineers ignoring the established discipline of spam protection, which they know how to use, and building a system optimized for social peer ranking, sharing cat videos and trolling?
Point. Google needed a good competitor to Disqus far more than they needed a competitor to Facebook. Sadly, Plus is obviously a better Facebook than it is a Disqus.
But either way, it makes the Real Names Only thing more obviously false: you're making a general-purpose reusable platform and not a specific social network of your own. It's a "Social Layer", right?
In that case, forcing the users to adhere to a real-names policy instead of providing an official supported path for anonymity or pseudonymity sticks out as trying to push your users into a pattern that they might not find a natural fit for them. And by "users" I don't mean the commenters, I mean the pages to which the comments are attached - if I want to allow anonymous/pseudonymous comments attached to my channel or page or whatever I have a Plus thread associated with, why doesn't Google support this?
Really the underlying problem here is that "Google+, the unified platform/identity system" has the same name as "Google+, the social network which lives at plus.google.com". People just blank out anything they do/say due to the assumptions which arise from conflating the two.
Let's say I have an anonymous pseudonym used on a number of other sites. I can now have it on Google+, with one big difference: it's no longer anonymous. Google will know who's using it because of their real name policy, and can then put two and two together across sites they don't own.
Anonymity means no-one knows who you are, not "no-one except Google."
You don't need a G+ Profile on your @gmail address to create G+ Page pseudonyms for Youtube. Your main address will continue to go plus-less, and other services which strictly require a Real Name/G+ profile (like Places/Play reviews) will continue to nag you to create one.
... I did not know that. Obviously, from my post above. Yay, I have a Plus page with a nickname! So, can I comment as Pxtl? Can I do that on Android play store reviews?
Additional point: Google's now chasing Facebook's stupidity--on Android. Facebook put out an idiotic failure of a launcher based on Facebook messaging. Well, now Google's following suit with an idiotic failure of a launcher called Google Experience Launcher on the Neuxs 5. Everyone's still crowing over it (because few people actually have it or have experienced it's uglyness), but it's truly atrocious.
(as you say, there's no compelling reason for them not to)
Right question: Why did they release it in the current state, which is, I think it's fair to say, 1) a disaster and 2) technically rubbish for all the reasons in the OP.
You should be asking: Why, when building a cross-site system to leave comments, are their clever engineers ignoring the established discipline of spam protection, which they know how to use, and building a system optimized for social peer ranking, sharing cat videos and trolling?