Dortmund have brilliant youth scouting and Klopp is really great in turning promising talents in very good players. That's imo a bit different to a great youth academy, but I agree with your second point. It's difficult to classify the players. Özil played 5 years in Essen's youth teams and 1 year in Schalke's, that's imo not really a Schalke youth product, even though he would be a homegrown player for Schalke if we go by UEFA rules (the player needs to be 3 years at the club between the age of 15 to 21, if I remember correctly). It's more difficult with someone like Kroos for example, who spend 5 years at Greifwald until he was 12, then 4 years at Rostock and then went to Bayern at the age of 16. All 3 clubs deserve some credit, imo, but according to UEFA he's a homegrown player only for Bayern.
You are right on that. Its the same guide line I remember.
It is easy to mistake Dortmund for a club with a great youth academy from the outside, because the first team features several young talents and Klopp is a coach that is known for allowing players to come through the second team into the first team. Our second team, which functions mostly as our U23, is actually pretty decent, being besides Stuttgart the only second team to play in the third German league. The problem is, that even in that team only a fraction originated from our own youth teams. The development in the first two teams is really good, the problems start sooner. Basically in the department under 18 we clearly lagging behind the top academies Bayern, Stuttgart and of course Schalke.
This can be seen at the actual crop of players, who came through the second team and are supposed to play a role in the first one. I would say, that there are currently five players in that class: the offensive Midfielder Jonas Hofmann, the (former striker now) Fullback Eric Durm, the two Centerbacks Marian Sarr and Koray Günther and the striker Marvin Ducksch. Only the last two are actually academy players of Dortmund. The first three all came at the age of 18-20, which shows the normal patter at Dortmund.
In the end, the officials somewhat neglected the academy for some time and put too much trust into their scouting, which results in a lower overall quality of U18 players. This was changed about two years, when they started to invest more there. However, this investment will take more time to bear fruits.