Our JEE apps were deployed to these app servers with very little internal support or expertise that very often had devs having to physically log onto production hosts and figure what in the world was wrong, restarting the app server, grepping logs and in general having to learn about these app servers (and usually just shrugging their shoulders at what went wrong). The sum total of things you had to know to keep the JEE deployments up was as much as you had to know about Nix processes PLUS you still had to know all the Nix stuff, except none of the JEE infra was built out since the app servers were just these monstrous processes with hundreds of db connections and thousands of threads.
My team long ago ditched JEE style deployments and have our apps all managed with the batch processing system and have been none of the better for it. Some* of those apps use Spring/Boot but I we've been doing a decent job in the code reviews of just rejecting anything too auto-magikal. Other teams that have stuck with these massive app-servers have stagnated since the deployments are so frail, no one dares make large changes. This is mostly an institutional problem but still the end result was sticking to simpler JavaSE stuff has led to way more productivity.
We ended up in framework hell. In response, we ditched all the frameworks we were using, went to pure JavaSE, and ended up with a (much!) faster, more reliable enterprise application that was far, far easier to maintain.