Actually, this I'm not entirely sure about. In my last BG1/SoD playthrough I made a conscious effort to keep all NPCs who appear in BG2 alive, but if key characters like Minsc, Jaheira etc. are dead in BG1, they will be mysteriously resurrected in BG2 anyway. The one NPC whom I killed in BG1 was Baeloth, and he remains dead in SoD (to a point... When you enter the map he's supposed to be found, you see a notification saying "Baeloth: Dimension Door" so is that meant to be interpreted as 'he's alive, but he's fleeing from you because you killed him before'?)

Probably the easiest way to test this would be to kill Safana, then have Imoen in your party before importing to SoD, since if Imoen is in your party, she gets automatically replaced with Safana as the party Thief.

I can actualy think of a good example of this. In SaGa Frontier 2, there are special attacks called "Arts" that can be learned either in party combat (by the standard SaGa method of selecting a simpler attack and possibly having a light bulb appear over the character's head, resulting in a new art being learned and immediately used) or in a duel (by entering the correct sequence of commands and getting lucky). Learning new arts in a duel, while possible, usually requires that you know the correct sequence ahead of time, and the way to learn that (in game) is to have a save where the art has already been learned, and then check its description.

It turns out that there is a special type of art called "Hybrid Arts", which combine physical and magical elements into one attack. Examples include Thunder Blade (does electrical damage with your sword) and Fire Bird (shoot a bird of fire with your bow, which damages the target and heals the attacker at the same time). These arts can only be learned in a duel, and the game never tells you the combinations before you learn them; as a result, most players who don't look for them will not learn them.

(Also, it's worth pointing out that the final boss is notorious for being difficult, and at that point there's no way to go back out and rest.)

(I believe the following SaGa game, Unlimited SaGa, actually relies on such meta knowledge, perhaps learned through trial and error or perhaps looking up information online. Also, said game probably feels more like a table top game more than CRPG implementations of TRPGs like AD&D do.)

I suspect that message is just an artifact of how the game is coded. Internally, the Baeloth of that scene is likely a different one from the one that joins your party in BG1, and therefore doesn't share the same dead property. So, in order to prevent a situation where the player sees a living character who was previously killed, the developers made the SoD Baeloth disappear before you could get to him. The mechanism the developers use, however, is probably something like haveing Baeloth use (probably via ReallyForceSpell(), which is one of the cheatier actions to include in an AI script) a spell called Dimension Door which makes him vanish (or at least moves him somewhere inaccessible through normal gameplay). This, however, creates the notification you mentioned.

In other words, the notification may just be exposing the internal mechanism used to keep Baeloth from appearing after being killed, rather than something that happens in-universe.

(There's other cases of multiple copies of a character; BG2, for example, has 2 Imoens (3 if you count the tutorial). Normally you would only ever see one at a time, but if you glitch past the cutscene that occurs when you leave the starter dungeon, you can keep that Imoen (the one with the belt that makes her unkillable, another attempt to prevent the situation where a character dies and returns later (though you can get around that by using Contagion to drain her Strength to 0, at least in classic BG2)) and still rescue the other copy of her in Spellhold.)

Precisely. :)
In my Shadowrun example, one of the unlocked conversation trees grants the player a bonus karma point (meaning that the three karma cost is reduced by a half), within the same mission. So this tells me that the developers were giving a big clue. (As far as I have discovered, there are no other conversations — in any of the three games — that require a minimum intelligence. It is never needed, except as a means to increase one of the dependent attributes, which are role-specific, like decking — a future version of hacking — and medical training for wound treatment.)
Bonus points for explaining the glitch. ;-P

This particular glitch is apparently quite tricky to pull off, but it looks like it involves dismissing Imoen, leaving Irenicus's dungeon (the exit only requires one character, but takes the entire party out), and then Imoen initiating conversation asking to rejoin the party right around when the cutscene is supposed to happen, breaking the cutscene. The speedrun I looked at just now mentioned something about putting a bear in a backpack somehow breaking the cutscene; I'm not really sure what's going on there.

If you want to see this glitch in action, I would suggess watching a speedrun.

Note that the version of Imoen that you get to keep this way:
* Is immune to many things, and is (meant to be) unkillable. In particular, no amount of damage will reduce her below 1 HP.
* If reduced to 1 HP, will leave the party (and can't be re-recruited).
* Still has Imoen's Belt equipped.

The other way to get two Imoens is to start the tutorial, recruit Imoen there, and then import the tutorial save into Throne of Bhaal; while there's a certain character who is removed from your party if in your party in the normal game, the developers forgot to do this to the tutorial characters. (Note that the tutorial characters have some strange stats, including BG1-style weapon proficiencies. Tutorial Imoen is good at setting traps, and there's a specialist mage with 25 Intelligence (because the developers didn't want him to fail to scribe a spell during the part of the tutorial that instructs you to do so).

What do the cool kids say these days? Crushed!
:)