Honestly, it is a big difference. I had the regular hatch before. When I transferred my stuff from my hatch to the MS3, the stuff I had on my hatch which occupied the hidden storage and about a quarter of the hatch open space, occupied more than half of my MS3's hatch space. Plus, like I posted above, the storage below the hatch carpet was totally taken away on the MS3, taking away additional storage. (regular hatch 17.1 cu/ft, MS3 16.5 cu/ft)
Now, I don't think it is the reason why they went with the hatch for the speed3 version, but imagine the sedan's trunk losing that amount of space the hatch lost.
I had a 00 Corolla which had 13.2 cu/ft of trunk space and my mom had a 97 Corolla which had 12.3 cu/ft of trunk space, and that is a big difference.