Help/advice on alternative keyboard layout / registry / new windows 10 thingy

Hi all,

My first post here, so first things first: Hello levelonetech community :-)

Background:
I have been writing with an alternative keyboard layout for years. I use Neo2, a layout made for the German language, but capable of writing many other letters as well via numerous layers (https://www.neo-layout.org/).

On Windows, there are two ways to use it.
a) via an Autohotkey script that changes input to the layout. This script can usually be run withouth admin rights. I use it at work on a win 7 machine ... works pretty good.

b) the proper way. is a combination of a keyboard layout .dll file copied into System32 and some alternations to the registry so it becomes available as a layout available in the windows keyboard settings. This method work as is, however for the full functionality, there is still another autohotkey script needed.

I have been using method b on my windows machines.
Instead of adding a new registry key, I would alter the existing ones in
HKEY_LOCAL_MACHINE\SYSTEM\CurrentControlSet\Control\Keyboard Layouts
to use the neo2 layout .dll.

The Problem
So far so good... this has been working for me since WinXP....up until some early Windows 10.
Since half a year, however, I notice in Windows 10, that the setup does not work anymore in these new "windows app thingy related stuff" .. It still works in the desktop mode though.

It looks to me as if Windows 10 is running two different "subsystems". An old one, where my registry changes still work, and a new one, for the apps, where it does not work.

My question now is
- What are these "subsystems"?
- Does anyone have experience with them?

I've been searching the internet, but don't even know what I am looking for. I am happy for any pointers in the right direction.

Seems like after all, I need to learn some new tricks...