Seems I discovered interesting bug.
The configuration is a bit tricky. I have a profile for GTA, where main layer has "L HAT" on arrow keys and FN2 layer has "L HAT left-right" and "RT+LT" on WASD via DKS because you cannot assign xbox controls onto layer.
This configuration works as expected - when main layer is activated, L HAT works on arrow keys. WASD works as buttons. When FN1 layer is activated - no xbox input is avalable. When FN2 is activated - RT/LT/LHAT is on WASD, no xbox input on arrows.
If after that I add some advanced key on WASD on another layer (main or FN3), for example another DKS or Rappy Snappy or Snappy Tappy or even Toggle - Xbox input will be working on all layers including FN1 that doesn't have any advanced keys on WASD. At the same time that second / conflicting advanced key works as expected only on one level, so only xbox controls are affected.
Somehow if same button has different advanced keys on two or more layers and one of the layers is used to assign xbox controls via DKS - second advanced key on different layer activates xbox control on all layers. This doesn't happen if xbox controls are assigned on main level normally.