Looks like I should have read the Capsule Github page. I didn't realize Capsule was caching the project dependencies. I could certainly see that making projects much faster to deploy.

Aren't the app servers and the embedded servers the same servers just configured differently? Standalone it is configured with XML and and embedded it is configured with Java code. It doesn't seem to me like there is much of a set up difference.

As far as I can tell, it comes down who cares more about the settings for the server, the people who maintain the machines or the people who maintain the code. If those people are the same then it sounds like it really doesn't matter.