Nice plan and really good stuff!
Yes you're right the sound source is obviously important and replacing the OEM HU is better. The only reason i didnt go down this route was due to software updates. As long as you are aware and don't mind, or if you know of a way to get around this, then its all good! I think Makkan is also replacing his HU so hopefully he can advise you more.
The only was of getting good bass is to fit a subwoofer in the boot, but the boots on these cars are so well sealed that you need something very powerfull to get into the car. Then you have a problem with vibrations etc. Plus you then loose a large chunk of boot space.
Thats correct but there is a better way to get loud and low without rattles. An IB install. Myself, kaigoss, makkan have tried this. Kaigoss and makkan have tried a few methods each and i think have an IB install presently like myself