There is a hint to make people aware of it (V13Comp):
{1001}{}{Hmm... I wonder why those are blinking?}
However, the break of atmosphere is the following line
{102}{}{Sorry, but we can't let you back in right now. Uh, technical problems. Try again later.}
This doesn't play anymore.
In vanilla you get this when using the computer twice (I think, i.e. first time doesn't trigger for some reason).
Removing this line is not optimal, but replacing it with a menu is even less optimal as it changes the atmosphere of the opening scene. The player is alone, in the dark, in a world never entered before (just after the cut-scene of the Vault's opening door) and now there is no other way but onwards.
Also the inability to return to the vault immediately creates atmosphere. A feeling of being lost and forlorn, with, again, no other way but going onwards.
Which means this is not only a bit intrusive (although adjusting the settings via a terminal is elegant in itself) but it is also a redesign of the opening scene (i.e. that terminal is supposed to be unresponsive to increase the feeling of being alone in a hostile world).
It's just not the best time to fiddle with settings. And it cuts a bit deeper to simply ignore it (i.e. a new player will open this setting menu and spend a few minutes reading it), which breaks the artistic set-up.
Still, I would be fine with a terminal used, but not the one controlling the vault door. Or if using that one, it shouldn't interfere with that opening message/atmosphere. I would prefer a terminal in a less intrusive place like the vault library (one of many, who cares). However, that would mean the “menu” won't be at the start of the game, which would be inconvenient, too.
Anyway, if protocol stuff like “settings, character creation, tutorial etc.” are included in actual game-play, they need to be woven into the story, otherwise they are always intrusive. Or they need to be disconnected from the game (like Killap's stone in RP mod, as mentioned (by Nibblenumb).)
Last, I think the reason this can't be done that easily in a menu (i.e. having this in the start menu would be optimal tbh) is because the list is rather long with several “settings” that go beyond a simple yes/no. Fitting all that in a menu screen could be tough. In Open Office the msg is 10 pages of options. Handling all that on a menu screen would probably need some rather creative design. Although having it all on one screen may be more convenient than manoeuvring a dialogue tree (?)
EDIT: Some mods use separate config programs (like Hi-Res or FoRes) for game settings. Isn't that an option (i.e. run it outside of the game)? Or is that Fo2 only?
