\documentclass{article}


\directlua{
function tilderise(n)
for nn in node.traverse(n) do
if nn.id==0 or nn.id==1 then % hlist and vlist iterate over the lists
tilderise(nn.head)
elseif nn.id==29 then  % if it is a glyph node change the glyph
print ('\string\n glyph=' .. nn.char .. '/' .. nn.font) % debugging
nn.char=126 % this is ~
nn.font=15  % force a text font as the classic math fonts don't have a ~ in this slot
end
end
return n
end

luatexbase.add_to_callback('hpack_filter',tilderise,'\string~ filter')

}

luatexbase.add_to_callback('pre_output_filter',tilderise,'\string~ filter')

\def\startzzz{\directlua{luatexbase.add_to_callback('pre_output_filter',tilderise,'\string~ filter')}} \def\stopzzz{\directluaa{luatexbase.remove_from_callback('pre_output_filter','\string~ filter')}}

\begin{document}
    \startzzz
    abc XYZ
    \[\phi+\int\frac{a}{1+x}dx\]
    \stopzzz
    abc XYZ
    \[\phi+\int\frac{a}{1+x}dx\]

\end{document}