Hmm it would seem the old linkpipes had clearance issues also - but the other way around, too close to the bike. Looks like they over-compensated for that problem.

Anyway I had another look underneath the bike today and theres no way to adjust the downpipes as they're bolted to the frame (through a rubber-bushed plate for removing vibrations), see image below. I wrote another email with my findings to MTC.

http://oi49.tinypic.com/2n1e740.jpg

Yeah Martin, that's exactly the problem....
I don't think its a particularly big deal, but its not ideal using the exhaust system as a stop for the stand.