I had the same problem that after removing the plastic moulding and installing a full size spare there is a "hole" in the centre of the wheel that the boot carpet, and anything resting on it pushes down into.
In practice, by the time the jack and the tyre inflater compressor, bag with hi-viz waistcoat, and old towel wrapped round everthing to stop it rattling is fitted in the centre of the spare wheel there is not much of a hollow left for the carpet to push into. My solution was to get a boot liner from ebay.
There are quite a few genuine Honda ones for sale (although a bit pricey) and lots of other cheaper liners that are tailored to fit. I found that the boot liner was stiff enough to stop anything loaded into the boot from pushing down into the spare wheel well.