After you call quotemeta, do some post-processing. For example,

my $expr = quotemeta 'foo.\E{2}\Qbar';
$expr =~ s{\\\\E(.*?)(?:\\\\Q|$)}{
  (my $unprotect = $1) =~ s/\\(\\?)/$1/g;
  $unprotect;
}ge;
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to handle embedded \E and \Q as needed. It removes any backslash by itself, and one backslash from every pair of backslashes; that should effectively undo a layer of quotemeta, if I'm thinking straight. I found that \E, when part of an interpolated string variable, is not recognized as a legitimate escape, so its use here is just as a flag for your post-processing.