Can a vim nerd respond with how to display-time-remap a normal tilde to another unicode codepoint? There are at least four tilde-like glyphs that may be cast by any middling magician of the Unicode elements: ~⁓〜˜
Looking at src/screen.c, the tilda character is hardcoded. So you'd need to patch it.
Perhaps a terminal application could do it then.
It's very easy to edit a font. So if the font is perfect except for the ~, just edit it and change that.