Got it to work! The following link helped me make the final adjustments, along with the test I did:
Summing it up, turns out I had to copy the server bundle to the root directory. And change the web.config file to call the root file. Here’s how the web.config file ended up, along with ...
From the messages in your question, I assume the app is properly signed with a trusted certificate. If you want to avoid the regular Java security prompt, consider using Deployment Rule Set. You can define rules based on the location of the app or its signing certificate.
When ruleset.xml is ready, package it into DeploymentRuleSet.jar and sign. Then deploy ...
You can use Windows Configuration Designer to create provisioning packages for Windows client OS.
Next, you copy the package to a flash drive and boot PC from it to provision Windows with required settings.
Check documentation here: https://docs.microsoft.com/en-us/windows/configuration/provisioning-packages/provisioning-create-package
It's perfectly acceptable to deploy an app without containers. We've been doing it forever and the procedures are well known and documented.
From your description it appears that you want to orchestrate deployment of your app and need a tool to do so. I would suggest getting started with something like ansible. It's very simple to get started but will scale ...