You are not making a coherent argument. Once you have decided you're building your server app in Java, it is MORE difficult to evaluate and decide Ubuntu, Debian, Red Hat, CentOS, etc. than it is to pick a runtime. Whether it has been like that "from day one" to use your term, is irrelevant. Secondly, having choice is GOOD. Yes it adds a bit of confusion but I'd rather have options than not. If you want some overriding authority to make all the decisions for you, go build on iOS.
Lol, you just can't leave this alone. Choosing a JVM is about 99% less confusing than the last 20 years of .NET Framework/Core/Mono mess and all its sub-projects (ASP.NET, Silverlight, WinFX, etc). At least in Java if you target v.11 you know to install JDK 11 (or higher). Meanwhile if you write C# v8 you need .NET Framework 4.8 to run it. Or maybe .NET Core 3 - which is now called .NET 5. Then over in Python land you've got IronPython, Jython, Pypy, plus the need to keep v2 as "python" on most Linux'es and "python3" for running/building new stuff. Don't forget virtual environments so you can pip install one version of a certain package while keeping it separate from a different installed version of that same package elsewhere. Java is super simple by comparison.
