Heh, I remember that old discussion being rather lively. I also remember that the user_confirm() in ZLib's early forms of check_version() was widely loathed (including by myself -- I was quite happy when I was able to eliminate it).
Removing that user_confirm() from missingManuel was the first thing I did back when I used it, because I dislike the idea of a script bothering you for more information after you already set it about its business. It's like sending someone to the store for milk, and when they get there they call you and ask if you also want bread. No, I would have told you that when I asked you to get milk. I would have said "get milk and also, bread." Your asking implies that I didn't know what I was doing when I only asked you for milk, which I resent. Or they call you at the store to say "How should I pay for the milk? I don't have any money." Why didn't you ask for money before you left?? I sent you to the store to get bread because I don't have time to do all the steps involved myself! Argh!
Emotional objections aside, philosophically I feel that a script is not meant to be a conversation. Normal CLI use of mafia is a series of commands in order, with complete user freedom of choice between them. A script is also a series of commands but with essentially no user freedom of choice. I guess what you're looking for is something in between, a mixture of the script's rigidity and the CLI's user choice, but none of your examples convince me that stopping automation but continuing to limit the users' choice while doing so is useful. All of those examples could be handled by injecting the user's choices into the script via either the initial parameters or script settings. If it's stopping because a choice needs to be made that it forgot to ask for up front, it may as well just totally stop and give full choice back to the user.
Consider installing older versions of Windows -- where the installer would periodically stop to ask questions -- vs. more modern versions that ask all the questions up front. The latter is universally preferred.
Emotional and philosophical objections aside, like Veracity said, I don't oppose the functions being available. In fact, I see some positive uses for them. Hellno made perhaps the most convincing argument in favor of these functions, since presently scripts run with their default settings until those settings are edited. These functions would allow a script to configure itself with user-chosen settings from the get-go, while retaining full automation after those choices were made.