So I return to Aran Linvail, the head thief, to see if he thanks me for removing Bodhi and her rival guild.

What does he say? He asks if I'm ready to set sail to Spellhold! (same dialogue and cut scenes and events as the end of chapter 3) Saying yes takes you to Brynnlaw with all the events resetted.

Is this a bug, or is it by design, so that you can go back to those unreachable places?

Hm... never noticed that, but i'd say it's not a bug. Maybe it is exactly like you said, for a chance to return to all those places you already visited, although i'm not sure what the use for that would be.

maybe for missed items?

That's a bug if I ever heard one -- why on earth would you want to go back to Brynnlaw? Your SOUL is gone, for heaven's sake! He should give you help to wipe Bodhi out for good (after some convincing). I sure wish that after having done that, I could go into his guild and kill him too. That would be right up my Paladin's alley.

Have you got the Darkest Day installed? I had the same problem myself.

I wonder what happens if you head back to Brynnlaw. Do you get to fight Irenicus all over again or is the island just pretty much empty because you completed all the quests the first time round.

Not just Darkest Day, have you any mod installed? Then you might have one of them wrong installed.
I had the a problem (talking with Aesgereth in Watcher's Keep resulted me exp and I could talk with him later to get same exp again, but that's ToB) with Kelsey mod but I understood that it was my own installing problem.

That is a real SoA bug, it appears regardless any mods you install and it's solved in SPfixpack (http://www.sorcerers.net/Games/BG2/index_editors3.htm).

No, I (still!) don't have any mods installed, only the official patch. For this particular bug, it's not too crucial, since you can easily avoid talking to him.

Just curious: what does he say after you install the SPFixpack?

I don't remember actually, but nothing very important. Just one or two sentences.
The fix just sorts out the problem where dialog didn't "know" that player is in chapter 7.