The reasoning in the "staged break-in" theory about the rock does seem quite curious and backwards now we've examined it closely.
It seems like the reasoning must have been "We need the break-in to be staged so they can be guilty, but we need it to have been staged in a really stupid way so we can prove it was staged, so they must have thrown the rock from inside".
Quadraginta's theory that they could have leaned out the window and chucked a rock in from there, or the alternative theory that they just went outside and chucked a rock through the window, both seem a hell of a lot more like what you'd do if you were trying to stage a break-in. Amanda and Raffaele really must be criminal geniuses if in addition to their flawless clean-up job they also managed to fake a rock being thrown in, by throwing a rock out, in such an amazingly clever way that it scattered glass all over the inside of the house (because of the violence with which they threw it) and left a nice, fresh mark on the inner shutter (because of the violence with which they threw it) without leaving a similar one on the outer shutter which it impacted first (...wait, what?).
Whereas if they'd just chucked a rock in from outside, then climbed up the wall, there would never have been any evidence of a staged break-in at all... or so you might think.