Am I right saying that creating some special players saved on wages and you lost on some team ratings but it didn't affect your results too much?
That's right.
Im kinda thinking: due to lower team rankings your team doesn't play to it's full potential...
Maybe, it's hard to say. If team ratings affect performance, then yes.
...but due to some monster players with lower wages it balances it for you?
Yes, maybe we can put it like that.
Then there is another question following after this, is it worth investing in them unusually built players instead of just having all around balanced players which also positively affect team ratings?
Hard to say, probably depends on your style 
I don't think there is a definitive answer, there are good and bad sides to this, you get something and lose something. On one hand, with specially built players you can get very strong rim protection without having to pay monster salaries, you can save on salaries and get an extra player or two for the rotation, you can design specific attacking or defending tactics that most teams have no answer to. On the other hand, it's more difficult to create a functioning team; you never switch only one player (because at least one other player - or players - must switch his or their defensive positions too); so ideally, all players must somehow fit into your scheme, including backups. Because of this, it's also much more difficult to replace a player - if you have conventional players, you can sell somebody and easily find a similar, better or younger replacement; with custom players, that's almost impossible.
So it's actually much harder, I'd say, but it can be really fun 
I was going to say, it takes a lot of effort and in some way inconvenience (train them in different positions etc).
It's definitely fun and everything but I think you either have to have someone doing the training for you or to lose quite a bit before your team gets there.
Anyway, thank you for the conversation, you have shown to me a little bit more to this game.
I was actually looking for a mentor to improve my understanding of the game. Do you need a student with 10 years BB experience?