Q1: subtree is only needed if the root of a Git repo is not “Bedrock” itself". (ie: your git repo starts with subfolders like ansible and site). So for your initial setup, your subtrees are correct. Which leads to Q2
Q2: Each site should be its own repo and then create another repo for ansible too. So you’d have 4 repos going from your original example. Note that if you use repos for each site, you don’t need to set subtree anymore.
Q3: You’d need to run vagrant reload and probably vagrant provision too. This don’t destroy any existing data.