Just to clear up a few things here:
1. All A3's have a sub behind the passenger side boot panel, regardless of Bose or non Bose
2. Unfortunately they share the same cheap plastic enclosure, so I guess Bose have done the best they can given the constraints Audi put on them for cost and having to share this feeble sub enclosure.
3. By disconnecting the Bose EQ wire on the back of the HU you are not disconnecting Bose, merely taking off the flat EQ the Bose system provides as standard and getting back a smiley face EQ of the non Bosed HU. You still have the Bose amp, speakers and sub.
4. The Bose welcome on startup is a setting via VAGCOM/VCDS and is purely cosmetic, it means nothing.
5. The pic posted above is a stealth sub in an A4 Avant. The A3 stealth sub is below and the amp is hidden behind the rear speaker panel.
Plastic tupperware Bose sub
18mm MDF Stealth sub enclosure, 6.5" JL Audio subwoofer powered by 300wrms Alpine V12 amp
All details are here: