[HugThem]

   only the following is stored in ibdata1

You say "only", I say "clusterfuck".

Just look at the very page you linked to. It's a totally confusing concept that befuddles users and causes questions "we often receive", starts "panic", can "unfortunately" not easily be analyzed and you might need to "kill threads" and initiate "rollbacks" to fix the problems it brings.

MyISAM got that right. One dir per database.

[amaccuish]

Ok but I don't get why you're so obsessed with the fs layout anyway. You should mostly treat it as a black box. And the point of ibdata1 is safety, which as you stated higher up is a serious problem with MyISAM. Even if it's not oom situations, you'll end up stuck sooner or later. You have been warned.

[HugThem]

    You should mostly treat it as a black box

Again, check the very link you posted. People do that. Until shit hits the fan. And then they have to take that black box apart. Which is not easy.