In order to output column and row totals, I think the best way is to build it into the data structure in the first place. This means adding a little bit to the "while" loop that is reading the data:

my %from_to_bytes;
my %col_headings;

while (<DATA>) {
    ( $from, $to, $hh, $mm, $bytes ) = /^(\S+) (\S+) (\d+):(\d+) (\d+)
+$/
      or ( warn "bad format on line $.: $_" ), next;
    $from_to_bytes{$from}{$to} += $bytes;
    $from_to_bytes{$from}{"~~TOTAL"} += $bytes;
    $from_to_bytes{"~~TOTAL"}{$to} += $bytes;
    $col_headings{$to} = undef;
}
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By putting "~~" as the first two characters of the hash key for the column and row totals, those keys will come out last when you sort the keys for output (because tilde comes last in ascii collation). Then you just print the matrix in the normal way, with no further ado:

print join("\t", '', sort keys %col_headings, 'Total'),"\n";
for my $from ( sort keys %from_to_bytes ) {
    print (( $from eq '~~TOTAL' ) ? 'Total' : $from );
    print "\t$from_to_bytes{$from}{$_}" for (sort keys %{$from_to_byte
+s{$from}});
}
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(not tested)