Maybe I'm just being a simpleton, but I can't think of these as one monolithic console.
I mean, from a hardware-designer's perspective, OK. From a programmer's perspective, sure. From a modern collector's perspective ... well, maybe. Hudson's marketing tried to steer everyone toward thinking of them as one system, too.
However, from a user's perspective, especially from the period and especially in Japan, no way.
Users don't really care what's going on under the hood, and smart users don't care about labels. They care how much things cost, and they care what their hardware can do.
I don't think you could tell PC Engine users with a straight face that the CD systems, which until their twilight years were fantastically more expensive than base Hucard systems, were nothing but minor upgrades or missing puzzle-pieces that they had to have in order to say that they had a complete PC Engine. In both major regions, far more people owned systems that could only play Hucards than could somehow play CDs. Did this majority somehow only have half the console?
Furthermore, the base Hucard system as a practical matter couldn't do any of the fancypants voice/cutscene/redbook things that almost singlehandledly sold CD games. It's not some tiny sound upgrade. Let's be honest: CD games, by and large, were not possible on Hucards.
I guess it comes down to how you define a "console" and "console games". To me, there's a certain uniformity to the idea, or a certain standardization, and anything that causes one guy to be able to play a game and another guy to not be able to play a game violates that whole concept. By definition, it becomes necessary to say that these guys have two different consoles.
In the same vein, I don't think of the Famicom Disk System as being the same as the Famicom, either - although the line blurs just a little because of the way FDS games became producible as-is on cartridges. I also am not really impressed that the PCE-CD outlived the base system. Even if the 32X had caught on and outlived the Genesis, I'd still think of them as separate if closely related systems.