I recall the humble bundle guys saying that they tried to get NoE involved for months. You would think that they would be able to work something out if they were supportive of the idea. NoA had to deal with different currencies too. EU codes are also universal so it doesn't matter which country your NNID is tied to and it would be just a matter of adding another region.
Out of the 11 games included (Guacamelee!, Woah Dave! 3DS, Mighty Switch Force 3DS, Stealth Inc. 2: A Game of Clones, SteamWorld Dig 3DS and Wii U, The Fall, OlliOlli, Moon Chronicles, Sportsball, Gunman Clive, Bit.Trip Presents: Runner 2 Future Legend of Rhythm Alien Wii U) only Woah Dave! and Sportsball are trully problematic since they haven't been released in EU yet. This could be easily solved with a different game selection. Moon Chronicles also had a different publisher in the EU but I can't see why they wouldn't be able to reach an agreement.
True, MS and Sony haven't participated in a HB yet but their platforms are still more sales friendly and NoE hasn't done enough to compensate.
The minimum cut is % based and not absolute. Dropping from 1,99$ to 0,99$ is fine, dropping from 7,99$ to 0,99$ would actually make you lose money.