To do it without capturing and resubstituting, you can add a lookbehind:

s/(?<=\d)(?=(?:\d{3})+\b)/$sep/g;
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This also works:

substr($n, pos($n), 0) = $sep while ($n =~ /\d(?=(?:\d{3})+\b)/g);
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As does:

substr($n, -($_*3 + ($_-1)*length($sep)), 0) = $sep for (1..int((lengt
+h($n)-1)/3));
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