If you listen to Mary Bergin or other good whistleplayers back, say, 30 years ago, when Generations were the only whistles available (save for the Clarke C), you’ll hear that they are all able to play the octaves quite in tune. What people did back then was to troll through as many Generations as they could to find the best-playing ones, and if necessary modify these by packing the heads and doing a bit of carving on the holes and/or putting tape on some of the holes. To this day many whistleplayers will tell you that there’s no whistle quite as good as a really good old Generation.
I still play the Generation C I got around 1980, and I’ve yet to play a C that’s its equal.
Here’s Mary Bergin playing a Generation. The octaves are just fine.
https://www.youtube.com/watch?v=v4hos7ZkRl8
To save the trolling, and the work of doing the modifications, you can get a modified Generation whistle from Jerry Freeman. I don’t know how he does it, but his Generations have the octaves in perfect tune. A common problem with whistles in general is to have the two octaves in tune, except for the D’s. Oftentimes if Bottom D is good then Middle D will be sharp, or if Middle D is good then Bottom D will be flat. Jerry Freeman’s whistles somehow correct this issue too, and every single note will be true.
Or if you want to get out of the Generation thing altogether you can get a high-end whistle such as a Burke. A Burke D, in aluminum or brass, with narrow bore or wide bore, will have perfect octaves and quite smooth even voicing. Over the years I’ve noticed that people coming to the whistle from the Boehm flute (or Recorder) tend to love Burkes.
Traditional whistleplayers tend to like Sindt whistles, if they decide to go to a more high-end whistle. I have a Sindt D and it plays like the very best old Generations do.
With the Burke you can get a thumb hole, because as you say:
“The thumb hole… unifies the fingering with the silver flute, which is easier…”
However the vast majority of whistleplayers find the traditional 6-hole whistle completely satisfactory as it is and do just fine without a thumbhole. A whistle can never be a Boehm flute, and trying to make a whistle play like a Boehm flute is, to not put too fine a point on it, a fool’s errand.
With a good whistle, in the hands of a good player, the crossfingered C natural is quite in tune and the tone of the crossfingered note is considered by many traditional players to be as good as, or better than, the tone of other notes.
The Baroque flute used many crossfingerings, and these crossfingered notes had a special tone colour, which was used to excellent effect by many Baroque composers. Needless to say most of the special colour of Baroque flute music is lost when played on a Boehm flute (the very goal of the Boehm flute is to make every note sound the same as every other note).