Because that's how it is

It's simple as that, really. It's just obvious it's a factory replacement and they sure as hell won't be adding any features / complications just for that one building. I just don't see any point to explain this simple fact. In V you get Gatling guns as soon as you enter industrial (while may not even have invented gunpowder) and your caravels and frigates have cannons, again, without gunpowder. That is just one example of Firaxis's immersion priority for you. But OK, in order not to come out as a arse, which I'm not trying to be, let's "rationalize" my position. That's the CivFanatics way after all.
You ask "did they say that it replaces it in the tech tree?" ...as if they ever say that when it in fact does, in other words basically always.
Now I do like the idea of UB's not being a replacement, but rather an addition, which will give a civ an option, two possibilities to fill the "X" slot in certain "X" district. In that case it would indeed be possible for the unique variant to come later.
BUT... The UB's would need to be VERY different from the buildings they repl... add to, to justify it being an "addition" rather than "replacement", otherwise (UB being just a buffed better version, which they always were) it will be redundant, useless and not at all fun mechanic.
I don't see that happening, seeing as electronics factory has buffed production and culture (bonus), in other words, better factory. Now of course we don't know yet how factories work, perhaps it is quite different to electronics factory, justifying building them instead in certain situations, but I doubt it.
The notion of upgrading a factory down the line (rather than additional building theory) I find unlikely too. Why? One building? Just for Japan? Is it upgraded automatically or do you need to use money / production time? I hope automatically, but... why? Why would they bother? What would it bring in terms of a working mechanic? Immersion for us? We all know that's not even slightly good enough for Firaxis to justify it. Funnily enough contrary to your thinking, I think that if that was the case, they WOULD actually mention the tech tree. Probably not explaining it well, confusing us even more, but nevertheless something along the lines of it being available at electronics, but never mentioning that a factory is available earlier.
In the end, I find the idea that they'll just rename it at some point much more plausible.