I am not sure that LLMs change much with regards to malleable software. A lot of software used to be somewhat malleable [1]. But that got removed, because it wasn't A/B testable or it wasn't the most easy implementation thinkable. Those two points are not changed by LLMs. Therefore, I doubt we will see a resurgence of malleable or at least configurable and scriptable software. Although, I would love to see it. Even those small features to adapt the application to your style of working instead of the other way around was extremely useful, imho.

[1] There was a time, when it was considered a standard feature of a UI that you could change keyboard shortcuts and toolbars. MacOS and Mac OS X even had an API that end users could use to script across multiple applications. Amiga OS had something similar based on the language Rexx.