The issue I have is why can't I use balls from my own inventory when I run out ?
I agree. This should be a given option.
Or... as far as I know, the rules of golf allow you to switch balls when you hole out and before hitting your 1st shot on the next hole. It should be the same in the game as well. When you run out of the ball in the middle of a hole, you finish the hole with the freebie.
I doubt this will ever happen though, since it would require more programming from the part of WGT as Walt pointed out.