I skimmed through Part 3 and it's basically saying that app servers are hard to deploy, maintain and dev against and you should be using Spring Boot or Dropwizard instead to create applications with the services you require.
App servers have historically been hard to deploy, maintain and dev against. There has been a huge amount of progress in the last few years. Based on my experience, Java EE / Wildfly is actually easier to develop with than Spring Boot.
These servers are just unzip == fully installed things. We have them checked in and just deploy them automatically whenever there's a need for an update, pretty much as every other library out there.
I wonder are we missing something or do people just wrongly think there's "something" difficult, where there's no need at all for things to be difficult?