Height is not used by the game engine. The way to think of it is that a 5'6 player who has average rebounding skill has a 48 inch vertical leap, very good timing, knows how to box out his man, and has strong arms and hands. A 7'4 player who has average rebounding has learned how to lace his sneakers. Put them both out on the court together and they both have about the same chance of getting a rebound.
This is even though the 5'6 player might be a much better rebounder than most 5'6 players, and the 7'4 player is much poorer rebounder than other 7'4 players.
When players are generated, height may be taken into account, simply by tending to give taller players better inside skills, and shorter players stronger outside skills.
Height does have an effect on training. A taller player will improve somewhat faster at inside skills, and a shorter player will develop his outside skills faster. So if you had two players with identical skills, potential, age, but one was 7'0 and the other 6'0, if you trained them as centers, the taller player would develop faster. And if you trained them as guards, the shorter player would deveop faster. I don't know how much difference there is - I don't think it is huge, like one player would develop twice as fast. But it might be like 1.2 or something similar.
I woudn't worry too much about a 6'6 PG. He might develop some skills just a bit slower than a shorter player, but would develop other skills a bit quicker. I think it helps for all players to have good rebounding regardless of position.