The way the game was programmed those other balls are exactly the same as the free golf clubs that are still in your inventory but not "in your bag" while you're playing. They're simply not on the course with you.
Switching equipment in the middle of the game is not allowed. The starter ball is something that EVERYONE has so it was hard-coded as the default replacement so people could at least finish whatever game they were playing.
The programming required to allow substitutions at the discretion of the player would probably create so many other problems the game would become totally unplayable.
There is also a financial incentive for WGT NOT to allow it. Players around the world have millions of dollars in unused balls sitting in inventories. Allowing players to use them up as replacements would reduce ball sales accordingly.