In Dark side, next to the fountain of Int in the north, there are 3 thrones: on one of them is Xanathus, on another a mage that takes the treasure map from you. The third one is empty. Is the empty one part of a quest I missed?

Yeah, I was wondering about it too, back in 90s. Neither me nor my friends found anything there. When I was replaying the game (~2008) I couldn't find anything there too. But this time I spent some time looking for it over the Internet and still nothing so I believe it's just empty. Perhaps some content was removed from the final version? Who knows...

Thanks. These little things in games drive me nuts sometimes...

Is this in Area D1 or E1?

There is nothing of note for E1, however D1 seems to have remnants of a removed quest. There are 4 lines of blank text (just a space) and 2 lines with the text "Delete me." There are no extraneous events.

To stick on topic, the one thing I don't figure out was that in order to activate the "logic of the town" and therefore getting access to magic and the rest. You just need to use a magic coin on a well. If you plan to save it for later, it will screw the logic, and therefore, the game.

But the game was fun, but this should be patched.