Do not replace or delete any binary files if you do not need storage. In this case, there is too little mileage in their removal.
You can simply do 3.1 by default:
defaults write com.apple.versioner.python Version 3.1
There are other ways to ensure that you are using 3.1 by default, I have not used them.
export VERSIONER_PYTHON_VERSION=3.1
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