Unfortunately, you cannot change ~ to any other character.
If ~ listening to you, you can hide it with the NonText highlight group, which is used to display them by setting the foreground color with the same background color:
:highlight NonText ctermfg=bg guifg=bg
Unfortunately, this also has consequences, see :h list for an example.
Coming back, I’d better adapt to the tiny ~ Some people think it's beautiful :)
PS Based on Josh's discovery, they discovered issue # 4181 in neovim repo
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