So simple to do with minimal prerequisites (one core module, Time::Local):

use Time::Local qw< timegm >;
while( <> ) {
    my @when = split /,\s*/, $_;
    for( @when ) {
        my @parts = /([0-9]+)/g;
        $_ = timegm( reverse( $parts[0]-1900, $parts[1]-1, @parts[2..5
+] ) );
        $_ += "0.$parts[6]";
    }
    print $when[0] - $when[1], $/;
}
__END__
2017-01-09 05:08:04.575804, 2017-01-09 05:08:04.319338
2017-01-09 05:08:17.093719, 2017-01-09 05:08:16.840292
2017-01-09 05:12:48.629407, 2017-01-09 05:12:48.372687
2017-01-09 05:13:25.315665, 2017-01-09 05:13:25.061834
2017-01-09 05:14:08.171994, 2017-01-09 05:14:07.916187
2017-01-09 05:17:03.182747, 2017-01-09 05:17:02.929309
2017-01-09 05:18:46.561289, 2017-01-09 05:18:46.305743
2017-01-09 05:19:09.772227, 2017-01-09 05:19:09.518975
__END__
0.256465911865234
0.253427028656006
0.256719827651978
0.253830909729004
0.255806922912598
0.253437995910645
0.255546092987061
0.253252029418945
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