My ED30 is exactly the same, and has been for over 3 years without getting any worse.
I asked this on the TFSI Tuning group facebook page a while ago. A few people had the problem, but no one had any answers.
Weird thing is, with VCDS hooked up on the ignition timing channel, when the rumbling occurs....at 1000rpm....the ignition bounces all over the place. It's almost like a 1000rpm limiter kicks in.
I had a Helix clutch put in a couple of years ago, along with a new DMF, no change.
Mine is also remapped and has uprated engine mounts, which doesn't help, but again, no change.
Just another odd ball quirk these cars can exhibit. I'd love to get it sorted as it's been pissing me off in traffic for years!! I just don't know what the fook it is though.