Windows-Inform7 VS gruescript

Anyways, back to your original question, by "use user prompts" do you mean having the player typing in "use silver key on old door" and the like? If so, Twine isn't really designed for that. You could do it in Twine, but you'd be better off using something like Inform 7 (Wikipedia), which is actually built to create games like that. However, I should note that Inform 7 is not well supported, at least not currently, with the last release of the engine being from late 2015. If you do decide to develop with it, I'd recommend using an Inform 7 IDE (Windows, MacOS, Gnome) to help you write your code.

Very detailed writeup!

I'd like to add that, perhaps surprisingly given how niche a field it is, the interactive fiction community keeps producing new languages and tools. In recent years, two new parser game programming languages have appeared: Dialog by Linus Åkesson (https://www.linusakesson.net/dialog/docs/index.html), a full-featured language inspired by Prolog; and Gruescript by Robin Johnson (https://github.com/robindouglasjohnson/gruescript), simpler but focused on creating web games, playable without writing, with a verb+object model like parser games.