Possible, yes. Reasonable to assume? I don't think so.
The issue is that we had that for a decade or two already: people who lived through the era will tell you more, but Smalltalk environments and Lisp Machines already realized this "malleability" to the extreme and... died. We got DOS instead; the rest is (a pretty shameful) history.
Emacs is just about the only artifact (along with Squeak-derived Smalltalk-likes) of the era that still exists and is in popular use. The PC revolution killed interactive, vertically integrated, fully programmable environments. It happened because of hardware limitations of the time, but the consequences are cultural: the LispMachine-like environment simply faded from the collective imagination of programmers who learned programming by writing "resident programs" for DOS in assembly. It didn't happen immediately: DOS was sufficiently open for modification that (if you knew x86 assembly) you could mold it to your preferences, but the hardware wasn't powerful enough to do much with it. As hardware advanced, PC OSes ossified, adding abstraction level after level in both hardware and software. Early Windows was trivial to dissect - I remember WindowBlinds, a set of apps that transformed Win 95/98 into almost anything you wanted. I recently checked, and nothing like that is possible in the recent Windows versions. GNOME on Linux seems to have followed the same trajectory (fortunately, there are still a few other desktop environments there).
So I don't think the "malleable software" is going to return any time soon. We have not only rigid software everywhere - we have 30 years of shared culture of developing and using such rigid tools. With the size of the programmer population, changing that culture in any meaningful way seems very hard. There will be people who rediscover Lisp Machine ideas, there will be a segment of users swearing by Emacs and similar apps, but we'd need a revolution in corporate and educational policies to get anywhere beyond that, I think.
As an Emacs user, I can testify that it's a game-changer. Codex CLI paired with `emacs --batch` is perfectly capable of setting up, developing, and testing just about any kind of extension you'd want. And with packages integrating LLMs into Emacs, you don't even need an external harness - open a buffer, type a prompt, get a useful extension or customization. It really works quite well.
But I stand by my opinion: Emacs is just one piece of software, not completely unknown, but rather niche, all things considered. Almost no other app supports seamless extensibility at Emacs' level (not even web browsers come close, and not by accident - it was a conscious decision to drastically limit what plugins can do).
Most programmers don't feel the need to make their apps easily and deeply extensible. Most users don't feel the need to extend their apps - even simple customization is rare. Most product owners don't want users to have "too much" freedom to change things.
So, while LLMs do give us a realistic path towards making extensible/malleable software attractive to users, almost nobody is taking that path right now. Realizing LLMs' potential in this area requires large parts of both the user and developer populations to recognize the possibilities and then actively pursue them for a few years. For now, it doesn't look like anything like that is happening.