My DD is a catcher and has been taking instruction for a couple of years now. One of the unbreakable rules is never throw from your knees to any base. She claims it will eventually hurt the shoulder. Boys can get away with it sometimes because boys are usually stronger in the upper body than girls, so they can get away with it. Girls aren't as strong generally and she can strain and damage the shoulder given time. It won't happen right away but given enough time, it will. (Our catching coach is a former college catcher.)
The other reason, our CC has told us not to throw from the knees, is by getting the core muscles into the throw, the catcher can get a stronger and more accurate throw than from the knees which are all arm.
Our CC doesn't even want my DD to throw it to the pitcher from her knees just to keep the "no knees" thinking ingrained.
We have been taught there are two stances, one for "runners on base" and one for "no runners on base". Most coaches in our area have kids use the "no runners on base" stance and almost never teach the other stance. Our CC has my DD strictly using the stance for "runners on base" for all situations. It's a better stance that allows for more versatility and flexibility behind the plate which is needed with runners. It is also the harder of the two stances to master and get into muscle memory. It is also the more critical one to get into muscle memory according to our CC because if you're throwing out a runner, you want it automatic. She also feels that stance is more appropriate for younger ages because the accuracy of the pitchers isn't quite there yet and it gives the catcher more ability to move and block.
We have had an ongoing conflict with my DD HS coach who doesn't quite understands catching (Coach's words, not mine). Simply, the ego got in the way of reasoning. The HS coach tried two other catchers to catch "the coach's way" which isn't correct at all. Both games were a disaster (and we lost). The catcher was limited by the stance and could not react to anything but a meatball pitch. Our conflict is my DD refused to change to that way and wanted to stick to her training (and for good reasons). Yesterday, the HS coach put my DD in a catcher and she did an awesome job and did it way she was trained. (And we won as well, coincidence? Not completely.) A couple wild pitches got by her, other than that she was a wall. Being in the "runner-on-base stance", the other team's coach saw my DD was ready to gun it on every pitch (and she has a canon arm) and they didn't attempt one steal except on those few wild pitches. (I think we converted the HS coach yesterday.)
Got off on a tangent there, but the point is proper instruction early on is essential to proper development and injury prevention. Catchers get beat up enough and work extremely hard with all that gear and stuff.
Just my 2 cents...