Another variation on the "don't add the line to your string in the first place" concept, rather than using eof, would be to read the lines into an array instead of a scalar, remove the last entry from the array if it matches the regex, and then join the (remaining) lines into a single string:

my @lines = <DATA>;
if ($lines[-1] =~ /^##/) {
  pop @lines;
}
my $slurp = join '', @lines;
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