Honest question, honest answer-
It matters a whole heck of a lot that this is a basketball game.
I've played basketball for most of my life, and have followed the NBA and NCAA for most of my life, besides a short stint where I lost interest, but then I read Bill Simmons' book of basketball in 2011 or so and was reminded of how epic so many of the match ups were and still are. So I began a search for a game where I could manage a team, set lineups, run the financials, etc... I used to play Microleague Baseball as a kid, and always hoped for a Microleague Basketball, but one never surfaced. I've always enjoyed forming a team, using different strategies to outplay my opponent, and seeing the stats develop throughout the season in every sports sim I've played.
First I came across a simplistic NCAA simulator that was pretty fun, but was more of a plug n' play. Then, I found Buzzerbeater, and have been having a great time since. Part of what I was looking for (besides the things mentioned above) was a way to create a team with specific builds that would be ideal for the style you want for them to play. Like to have insanely great passing bigs such as the Bird/Walton Celtics, or a crazy rebounding, slashing, and fast breaking team like Drexler's Blazers, or an ugly defensive minded half court team such as those that materialized in the Knicks/Heat battles of the 90's (I hated those games, but thinking back, they were sort of amazing in a way).
So, you bring up a solid point. Playing guys out of position to get better at said position has nothing to do with real basketball. I'm not going to argue with that. Dwight Howard would never be forced to play PG in an NBA game to improve his handles, and Steve Kerr would never be selected to play down low to improve his shot blocking.
All that said, I don't care. That's what we have to do to train our players in the fictional land of Buzzerbeater. Then, we can play everyone where they should when it counts. The playoffs... or in games where you really have to win in the stretch run and cup games.
As a basketball fan, I don't mind having to set my lineup in a way that I wouldn't have to do in real life in order to improve a player's specific out of position skill. I cringe sometimes, like on my Utopia team when I have to set my PF at SG and hope he doesn't turn the ball over 8 times on offense (but of course I have him guard the opposing PF), and think "this may not go so well", but those are the rules set out in order to achieve my objective of making him better at a guard skill, and I am alright with that. It is a divergence from reality that was created at some point by the powers that be in order to add challenge to this particular game in the realm of training players.
This is still a basketball sim. If it wasn't, I wouldn't play it. It is a basketball sim with a quirky training system that makes you do weird things in order to train players in certain skills. You can always not do that. You can always just train your players in skills that fall under their current position nicely. You could probably build some serious beasts that way. In fact, you probably have (as you are a very experienced BB manager).
In your last full paragraph, you reference people like me who like this game for not being about basketball prior to hearing my actual reply to your opening question. I absolutely like this game because it is about basketball. This basketball fan is not deterred by the wonky training system, and does indeed find it adds to the fun.
It's all still basketball. You're still playing your PF at SG to improve his JR. You're not suddenly playing your Power Forward at 3rd Base to improve his Penalty Kicks.
Iguanadon