@F8L - the little rubber feet idea is a good one. I got double sided tape and a cheap floor mat (soft rubber) from Costco. A pair of scissors and 30 mins work has removed the rear end ones.
Firstly check the catch, if you can adjust it "down" then do so, this makes closing the hatch harder but it does lock it more securely against the existing buffers so the rattle goes. Careful though, adjusting it too far means the "slam" is too hard and the rear won't latch properly. I had to leave mine loose as Mrs A has to close it and has less strength / anger about it all
To solve this add some extra rubber to the existing buffers. Eventually this will drop off so you will have to renew it. There are 2 buffers (I think) on each side.
After that the next one is the ridiculously idiotic design of the under floor storage tray in the boot (trunk) - insert loads of buffing in there. Bash your fist firmly against the boot floor to detect rattle areas and pad them out. For best results empty everything from here and add them back one at a time and repeat the thump test padding as you go.
While you are there check if the boot cover is secure at both ends (even the dealers don't know how to fix it properly) and the rear seats if you have folded them at any point.
The glove box is a notorious rattle area - seriously these interior designers are morons. Small buffers inside the lower and upper lid to hold the door "in tension" against the catch does it - there doesn't seem to be any adjustment, I've had mine in pieces to check.
The rattle in the centre console is also annoying. I think there is a relationship between the seat position (front to rear) and the buzzing that comes out but I haven't pinned it down yet. I have forced the rear of the "bridge" element up and pushed small rubber pieces between it and the console between the seats which seems to help. A piece of cloth between the seat and the console (try both sides) will often remove the rattle there too but it will return at some point for no reason.
Also check the cup holder / cover section.
The rattle behind the steering wheel is impossible to get at as far as I can see, if you manage it post some photos. I suspect some wiring is rattling against the console when cold which is what was happening in my Fabia. In that car I too out the radio and repositioned some foam behind and it went away.
I've driven cheaper Toyota models (e.g. Auris and even my Aygo) and they rattle far less than this. For a car costing the equivalent of a decent BMW or Merc here they need to do a lot better - Mrs A is not considering one for it's replacement at all.
EDIT - and the dealers don't think it is a problem. Muppets.