In one view of the world there is no such thing as “best practice.”
Instead, the view is “what others do might work for you too, depending upon your situation.”
My only caution about VCS with Integration Server and related components is to be very aware of what the VCS support in Designer does and does not do along with ABE/Deployer. Version control and builds with packages, adapters, config files, models, TN, etc. (depending upon one’s environment) is an undertaking. Do not assume it is trivial. It’s not hard, just more involved than what is usually initially assumed due to various constraints.
By “projects” do you mean independent components that do not share code? Are there any services/packages created that are shared? When you mention “1 giant cluster” what type of cluster do you mean specifically? These items may help with segregating components for VCS purposes.
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