Thanks. Your idea about tomcat with multiple domains might be a better idea than my idea of multiple projects. The fact that some site settings are shared was actually generally a positive for our purposes; however, I bet we could synchronize some of that.

We actually more or less have a cloned VM per site/project now (though the dev-ops stuff isnt as efficient as it should be). Unfortunately we are also charged per VM, which is really kinda silly for the actual use these 'sites' get and the cost hoping to avoid. Even with the clones VM, there's still a non-zero time cost with each new VM instance as well.

Does LabKey have any newer features designed to help bootstrap a fresh instance with some config automatically applies? If you're spinning up cloud instances perhaps this has been considered?