Just wanted to give a quick update here: it's actually an issue with Serato, which is not implementing the ID3v2 standard in this regard.
However, the unsynchronization scheme was initially invented to not irritate software that isn't aware of ID3v2 tags. So it's very unlikely that not applying the unsynchronization scheme would cause any harm. I think most — if not all — of the apps that work with audio files are ID3v2-aware now. This is also the reason why I think that Serato and others are unlikely to implement this anytime soon.
As a consequence, I've dropped applying the unsynchronization scheme with Mp3tag v3.06c to increase overall compatibility.