Latest update... found a thread somewhere on the forums earlier today (can't find it now thought) about a similar issue being caused by the stock vacuum line that goes between the T-piece and the wastegate actuator. This short bit of vacuum line makes a very sharp bend and collapses in on itself. Mine was a little bit squished - not too bad, but I thought I'd replace it anyway (with a longer hose so it can loop around without getting a kink in it).
And I think this has fixed the issue. Took it for a spin, it was a bit jerky at first but seems to have cleared itself (maybe the ECU re-learning). On the logs the wastegate actuator duty seems a bit smoother too.
I'll give it a few more days before I consider it fully solved, though... but so far so good!
Note: if you replace the vacuum line between the turbo and the T-piece too, like I did... make sure you push the restrictor pill in the new bit of vacuum hose. You'll need to push it in there with a thin allen key or something.