it took SQLite 310 seconds to insert

The SQLite docs say what you should do to improve speed: group instructions into transactions and eventually modify the "syncronous" pragma.

If you add $dbh->do('begin'); before your loop and $dbh->do('commit'); at the end, the insertion will take less than one second, as it should be.

use Time::HiRes qw(gettimeofday tv_interval);
my $start_time = [gettimeofday];
$dbh->do('begin');
for my $i (1..1000) {
    $st1->execute($i, $i * 2);
    if ($i % 2) {
        $st2->execute($i, $i * 3);
    }
}
$dbh->do('commit');
my  $elapsed = tv_interval ( $start_time, [gettimeofday]);
print "creation time: $elapsed\n";

__END__
insertion time: 0.263462
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