Illithids do not have an afterlife though. When they die their brains are eaten by the elder brain, not uploaded into the Matrix.

It isn't even actually death just the next stage of their life. Also "soul losing everything and joining the greater whole" is one of major themes for afterlife so either way. Illithids who died without it can later appear as for example postulants which proved they do in fact have souls, though those are more likely the illithid souls and not the original people's souls.

And in BG3 internal canon

Yes, it do conflicts with the other lore, especially that the only "proof" for it are the words of deity that isn't known to be very relible, and it observably conflicts with what we see in game, namely people turning into lillithids and retaining their persons. It more sounds like game handwave this issue.

Though you are probably right in the sense that this game thrown a boatload of new lore about illithids and since nobody really curate canon for D&D it will probably be like that, conflict or not.