Humans find thousands separators useful. You're asking humans to give up useful things because they're hard to program.
That said, I idly wonder whether they could be implemented with font kerning. The bytes could be 123456.78, but the font could render it with extra space, as 123 456.78.
I don't know if it's possible with current font technology, and there are probably all sorts of problems with it even if it is, but it might be vaguely useful.
I agree though that this can (and should) be solved at font-rendering level, not at an application level.