It is changing the ball. However the only other alternative would be a forfeit so I guess that WGT has concluded that to avoid forfeits they will default to the free ball.
I can see their issues with it but in reality I think that the game should just give you the option to buy more of the same balls, that message seems to appear at the start of each game when you don't have any extras of the brand you are using, or allow you to click on which type of ball you want to play. I suspect that since the equipment changes have to be made prior to starting a game, that WGT can't allow a ball change without allowed club changes midgame.
I just don't think this is a big deal, just check your ball stock before you play.