Here is how I carry and secure a full sized spare in my Mk4, which has no spare wheel well at all ,let alone a shallow one. Although at first sight this appears quite intrusive the height of the wheel is only about 200 mm (8") There is still enough room (IMO) for shopping and luggage. I can lay a medium sized suitcase on top of the wheel yet still under the boot cover.
I accept a mk3 is different to a mk 4, but I would have thought even the shallow well will reduce the wheels intrusion by a useful amount. It may be possible to level the boot floor to the same height as the wheel by using simple pieces of timber of a suitable thickness on the boot floor with an easily lifted false floor of hardboard etc. This arrangement might only reduce the remaining boot height by a small amount , or alternatively may give useful storage space hidden under the false floor, . The false floor would also contribute towards keeping the wheel secure/safe.
Has anyone with a shallow well done this and able to provide a photo , or some idea of the measurement involved?