How about this -

my @elem = split /\t/, $line[4];  # split
my ($id) = $elem[0] =~ /"(.*)"/;  # capture
$elem[0] = '"new_alias"';         # replace
if ($elem[4] =~ /\salias:\s/) {   # check
    $elem[4] =~ s/"$/, $id"/;     # append id before last "
} else {
    $elem[4] =~ s/_random text_\s/_random text_ alias: $id/; # prepend
}
$line[4] = join "\t", @elem;      # rebuild
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