Perhaps Quirrell is just counting on the investigators not being very careful thinkers. Lord knows the wizarding world is full of those.

But why leave the flask at all, then? It must be meant to make them think something else.

whoever it was died shortly after being arrested, and expected the vial not to be noticed.

Couldn't be. Bella's been there for twelve years - and they've been feeding her daily, they'd have noticed if she died "shortly after". And the fake body doesn't look ten years dead.

What potion, if found by the Aurors near Bellatrix's corpse, would lead them to a useful-to-Quirrell conclusion?

Any potion being found stops the Aurors from thinking Bella just died in her cell in the ordinary way from Dementor exposure. (An event that would be no surprise at all, in her state.) A potion indicates outside involvement.

The Aurors would think: someone came from outside, gave Bella this potion-bottle, which is now mostly empty but recently contained something, and now Bella is dead. It certainly looks like poison.

The big mystery is that Harry knows it's there, he must know what its part in the plan is, and yet he seems to think that the original plan was to make the Aurors think that Bella died from natural reasons...

Of course, another possibility is that the flask wasn't meant to be found...

The description given of Quirrel concealing it makes it clear it wasn't well hidden. In fact it was barely hidden at all - if a wizard is doing the hiding, "covered with a piece of cloth in the corner" isn't that amazing. In fact it's on the bed instead of being under it, so it clearly isn't being hidden. The only way an investigator could believe someone was trying to hide it was if he believed that poor, mad, dying Bella was "hiding" it in her last moments.