Okay, finally tested this a bit more.
First, a few observations:
* On a Touch 5.1.0, Amazon downloads thumbnails with a max height of 262, not 180. (Which might explain why the Cover View was already broken on the Touch with covers sideloaded from Calibre).
* On a PaperWhite 5.2.0, they have a max height of 330px.
* The thumbnails embedded in the mobi/kf8 file are still 180x240 (max), even when delivered to a PW, so, no need to change anything there.
* Indeed, when in Cover View, the Touch & the PW will discard the thumbnail if it's too small (I didn't bother checking px/px what the minimum height is, though).
* On a slightly unrelated note, no issue with the 'Personnal doc' banner. It only pops up if there's no exth 113 set. The PW is still friendly with our custom uuid

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Now, the good news: the Touch (again, 5.1.0) doesn't choke on x330px thumbnails sideloaded by Calibre. AFAIK, the Touch & the PW are the only models that rely on these, so I see no harm in bumping this to 330 in the default plugin

. (The only downside is potentially suffering from a somewhat crappy downscaling of the cover in the longpress popup, but then it's already not that great with thumbs downloaded by Amazon, so...)
That's what I ended up doing with this tiny patch.
EDIT: Remove deprecated attachment. Merged in 0.9.3

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