I know ofcourse that i gave a stupid example with Nc3 but i wanted to make clear how i think that the livebook works. So lets take you´re more realistic example 1.e4 e5 2.d4 ed4: 3.Nf3 after which you say "it then gives a bunch of moves for Black...only 2 ever get any play. So it's taking into account transpositions."
I think you mean the 2 moves 3...Nc6 (13202 times) and 2...d6 (2756 times). But in fact the most played moves in this position are : 3...Nc6 (2250 times), 3...Bb4 (423 times) , 3....d5 (338 times) and then 3....d6 (281 times). At least according to my database containing 13,5 million games (see attached printscreen). So that is what i mean when i say that the livebook counts transpositions leading to excisting positions in games instead what many people think the actual played moves in the given position.
(See also the second printscreen to see that after 3...Nc6 live-book gives 13.000 times played while my database gives 10 times more.) This made me wondering how chessbase counts in the live-book.
Refering to importing PGN-files you are completely rigth. I just wanted to warn people importing files from less quality. The way you do it is the correct way when you want to examine a certain variation. The only disadvantage is then that when you do it that way you can get the same position in different openings / databases when there are transpositions. But when people don`t mind that it is perfectly working.
I just want 1 database where i want to have a move order occurring after a certain position just once.
So not the following position examined in different opening-lines/databases
1.d4 d5 2.c4 dxc4 3.Nf3 c5 4.e3 cxd4 5.Bxc4 e6 6.exd4 Nf6
1.e4 c6 2.d4 d5 3.exd5 cxd5 4.c4 dxc4 5.Bxc4 e6 6.Nf3 Nf6
1.d4 d5 2.c4 dxc4 3.e3 c5 4.Bxc4 cxd4 5.exd4 Nf6 6.Nf3 e6
1.e4 c6 2.d4 d5 3.exd5 cxd5 4.c4 dxc4 5.Bxc4 Nf6 6.Nf3 e6
1.d4 d5 2.c4 dxc4 3.Nf3 Nf6 4.e3 c5 5.Bxc4 cxd4 6.exd4 e6
1.d4 d5 2.c4 dxc4 3.Nf3 c5 4.e3 cxd4 5.exd4 e6 6.Bxc4 Nf6
1.d4 d5 2.c4 dxc4 3.e3 c5 4.Bxc4 cxd4 5.exd4 e6 6.Nf3 Nf6
1.d4 d5 2.c4 dxc4 3.Nf3 c5 4.e3 cxd4 5.exd4 Nf6 6.Bxc4 e6
these and many other move orders all leading to the same position
So i want a clean database with the same end-position occurring once and not scattered over several databases arising from several move-orders. But that is my way of working, as already stated time-consuming but at the end efficient i think (hope

).