You're probably going to catch a lot of grief for not using the search function located over on the right ----->.
This has probably been the most requested thing on these forums for years but it's not going to happen. Those other balls are not "in your bag." Only the type of ball you start with is "in your bag". Consider all those others as being in your closet and not available out there on the course with you. That's just the way this game was programmed.
The starter ball replacement was put in since every player in WGT has it available to them and WGT was able to put that in as a favor to customers so they wouldn't be forced to forfeit or be dq'd automatically.
It's like wanting to break up iron sets. The programming wasn't set up to do that and any attempt to change it at this point will most likely result in an absolutely unplayable game due to all the glitches that will result from the programmers digging that deeply into the software.
The easy solution is available to you and WGT needs to do nothing. Don't start any important game or match with fewer balls than you might need. Use all those odds and ends in tournaments, practice, CTTH games, etc. where there is no penalty for just dropping the game and starting over.