My experience with Japanese - even the older generation, is that seiza isn't really any more comfortable for them than it is for anybody else. They're just a little more accustomed to the idea, that's all.
For example, making school children sit in seiza used to be a popular form of corporeal punishment.
The issue with many folks who did not grow up sitting seiza is not that it is uncomfortable, but that it is actually piercingly, acutely painful.
Different people's legs grow differently - I know plenty of Westerners who have long quads and hamstrings, small calves, and sufficiently flexible ankles to sit in seiza with no problem, even if they don't do it much until they are adults. But I have never heard from a Japanese person who actually felt intense pain sitting in seiza who had not had an injury.