I'm just wondering how he is projecting sound through a vacuum.
Assuming that there isn't more atmosphere here nearby the Praeses than we think there is? Perhaps akin to how they can move. Instead of artificial gravity or magnetic currents or coalesced particles etc, this is Church creating a localized and in this case sound-carrying (300 Hz, 3KHz, whatever) atmosphere between him and Alice. Or he's just really loud, a few thousand bels is beating down space into verbal submission.
If he's not creating some density for the two that supports human speaking/hearing frequencies, that could work too. It's true that normal empty space doesn't have enough density to support such sounds (in the human-hearing sense of it). But space isn't a total vacuum either, it's just a very thin medium that can carry only very long wavelengths. If he's sending at a low enough frequency and she is capable of receiving that. Sound, just not in the sense of human-audible. Him speaking and her hearing at something a few billion times lower than human limits, and certainly the two are not exactly limited to human specs. What problem might infrasound be to them, given how they are out here with essentially no protection against pressure and temperature (say, one side of them is -250F and the other +250F) and nothing to breathe. Which would also mean nobody but these two (and perhaps Sedna, if she wasn't too far away) could either receive or understand what he just said. Just like the others can't do what they are doing.
If none of the above, it could be via another mechanism entirely, which is displayed here in a way that approximates what we're used to, but is nothing like what is actually happening. Notional and figurative, not literal. Communication bubbles, presented in a certain way just for us the reader.
Oh, I'm not disputing that Alice would be extremely difficult to kill, and maybe impossible with even Church's pure strength. I don't think she straight up can't die, though at this point that's speculation.
Nobody knows if any of these are killable or not, but both Alice and Sedna have been damaged, and Church apparently not unduly put out by being encased within lava etc for thousands of years. We also know that at least in short time scales (geologically speaking) they haven't died. We don't really know about how many others there might have been or what happened to them if there were.
Although given that Alice seemed pretty serious in the flashback, perhaps she was tasked with killing/incapacitating all the others, and missed or spared Sedna. Or Sedna was another one doing that work. If Alice destroyed all the other special mechanisms, or there were more and some found an ending some other way, it would seem reasonable to think that most can die or be killed or be destroyed. If Church can't be, maybe not the two others either, or maybe only Church is an outlier. Or perhaps Alice neutralized him for some specific reason, and he could have been destroyed. Well, whatever she's planning on doing now, we don't know what it is or if it will work. 5000 years is a lot of time to change for better or worse.
As far as that, perhaps Alice was lying or wrong or telling Jedi truth when she said all the AI was destroyed. We don't know any of that either, but that she said it doesn't prove these three are not AI any more than it does. So, just more speculation.
That being said, why did people think that Church couldn't talk?
Given that Church has never spoken, it seemed likely he couldn't. Speculation. A tentative assumption. Of course, it's also possible he still hasn't (that what we just saw wasn't speech) or that he can only talk (whatever that entails) with something like Alice, in space, during battle, while near a Praeses.