What's the effect of the keyboard layout chosen in the operating system?

What exactly is the effect of the keyboard layout chosen in the OS?
If i wanted to configure my OS to use a cyrillic keyboard but not really notice it while using it (i.e. for me it should continue to behave like a QWERTZ keyboard), can i do that?

I believe in Chrysalis under Preferences → User Interface you set the Keyboard layout that the computer you plan to use the keyboard uses. So you would set that to Cyrillic. Then in Chrysalis you would set your layouts to QWERTZ. Then when Chrysalis flashes the layout to the keyboard it will handle sending the right key codes to the laptop.

I could be wrong about this. I have not tried it, but that is my understanding.

Setting the host layout in Chrysalis only affects Chrysalis. It does not change how the keyboard works, or how it sends key data to the host. It is purely for display, so that Chrysalis can display the symbols on keys that’ll end up being sent to the host.

If you then rearrange your layout to send QWERTZ nevertheless, then yes, you can continue typing that. However, importing the QWERTZ layout when the host layout is set to cyrillic will not do what you expect, because the layouts shipped with Chrysalis assume the host is US QWERTY, and Chrysalis does not do any translation. Doing so would be incredibly complicated.

Thus, the best - and pretty much the only - use of setting the host layout is when you intend to use that layout too.

My mistake. To be honest, I am still confused on what it does then. Are you just saying it determines what is displayed on the image of the standard keyboard below your layout on the layout & colormap screen?

Yep, it does exactly that.