The question about toiletting on a long flight really beggars belief. I love dogs, but can seriously understand that many passengers would not be happy sharing a flight with one who has to urinate and defecate in close vicinity. And of course those with severe allergies.
There is one thing you can look into. On some Boeing 747's configurations there is a separate area of the cargo hold where pets are kept, and there's a stairway in business class that people were able to use to visit their pets during flight, if of course you're flying business class.
As the 747's are being taken more and more out of long haul service it might not be so easy to find, and if they still allow people to go down to that area, but this could be an option for you if you really have to him/her fly with you (can't remember which of if mentioned). Recommend you look at US Airways, Delta, United and Air France as they do still have many 747 configurations in long haul service
(I even looked into travel by ship, but that too turned out to be inappropriate for him. We never made it back, and now that he has gone from elderly to ancient travel is out of the question.)
I realize that some folks have been lucky and had the rules bent by a sympathetic check-in agent but given that our vet was adamant that my oldie was not fit to fly cargo I couldn't risk trying to bluff his way into the cabin.
My healthy dogs have flown long-haul cargo many times without problems; the key is getting them accustomed to traveling in their crates, teaching them to settle. (Happy to help with tips on how to do that if you wish.) I use a professional shipping company to make the arrangements - I feel better knowing a pro has our backs.
That said, I wouldn't fly my dogs for a 3 week stint - that's too much stress to put them through in a short time.
I understand your hesitancy in putting your dog in kennels for 3 weeks - I, too, would never consider kennels for my crew. I have checked out a few, but found those wholly inadequate for my guys' 'special needs'. Rather, the dogs stay at home with a live-in sitter, or my husband and I travel separately so that one of us can care for the dogs.
Why not focus on finding a live-in sitter, where someone cares for your dog in your home? It will be expensive - around CHF 200 per day - but this is often the best alternative for pets who can't fly and who do not do well in kennels, as your dog stays in the environment to which he is accustomed. Advertise here on EF; there are indeed a couple of folks who offer dog sitting services.
Good luck with your travel plans.
ETA:
On the long haul flights my guys have done, ranging from 12-17 hours total in-crate travel time, they have never soiled their crates. Obviously I would not want them put through this often, or for a short trip. But for an international move, one day of less than optimal conditions (providing the animals are properly introduced to crate travel) is worth it to keep the family together.
You do not exactly see trains full of doggie doo
I've been on several long haul flights and been more disturbed by the flight attendants than by the small dog that's been tucked away at it's "best friends" feet.
As for the kennels here in Switzerland. They are truly amazing. Well the ones I used to use. My old dachsie was not a very well behaved or sociable dog but he loved going to the kennel and was actually much better behaved after every stay. The girls who used to take him from me when I dropped him off always loved to see him and he them. Why not give your local kennel a one night tryout and see how your dog deals with it?
Shorter than the train time Zürich to Hamburg, circa 9 hours or Madrid circa 20 hours