... just get "\000\005issueentrust.net" translated to "0,5,issueentrust.net" ...

Try:

c:\@Work\Perl\monks>perl -wMstrict -le
"my $s = qq{\000\005issueentrust.net};
 $s =~ s{ \A (.) (.) }{ sprintf '%d,%d,', ord($1), ord($2) }xmse;
 print qq{'$s'};
"
'0,5,issueentrust.net'
[download]

Update 1: But this sounds like an XY Problem; it that really all you want?

Update 2: Here's an unpack approach:

c:\@Work\Perl\monks>perl -wMstrict -MData::Dump -le
"my $s = qq{\000\005issueentrust.net};
 my ($flag, $tag, $issuer) = unpack 'C C/a a*', $s;
 dd $flag, $tag, $issuer;
 my $t = sprintf '%-6s %s %s', $flag, $tag, $issuer;
 print qq{'$t'};
"
(0, "issue", "entrust.net")

'0      issue entrust.net'
[download]

(Update: Changed  $remainder to  $issuer in this code example because this naming corresponds better to terminology used in the OP.)