If they had been instructed to maintain a lower altitude, that would have been said as such - European ATC units do not ask someone to maintain level at an altitude. That is a poor excuse.
I agree that harmonising EU transition altitudes would be nice, but the explanation about needing a ridiculous amount of ASRs to cover the wildly differing QNHs makes sense - I had never heard that explanation before and it seems entirely logical. All the same, a 6000' TA across Europe must be "doable". I still can't see how uncertainty over TA could be an issue in this incident - if cleared to a FL, then you know you're going up reasonably high, much more than 2000', and nobody would stop at 2000' out of EIKY if they had any situational awareness.