I don't really understand the backpressure issue, mine is basically a piece of 2.5" pipe turbo backwards and i havnt seen the hit in mpg. Could the ecu have become confused and not 'learnt' how to cope with the new set up? Cat damaged / blocked and making turbo less efficient? Maybe you could mock up a muffler out of steel wool or something add a bit back pressure. Like you say maybe the type of driving suits the turbo in different ways without the box...hmmm.
Really dont know, can't wait to dump the mufflerectomy though for a proper exhaust.
The cabin noise at contstant speeds are just annoying, its taken the please of driving the Leon away completely -
Hopefuly will book it into AwesomeGTI very soon, credit card is getting a good dusting down.