G'MIC-QT window is modal which means that active layers cannot be selected or changed while the window is opened. This also disables input from other sources such as the keyboard undo. This gravely limits functionality of the feature as applying functionality to multiple layers becomes overly tedious. The solution is to revert to the previous implementation of G'MIC-Qt which had the window set to be non modal, and thus, making it easier to use the feature.
This issue is discussed further here: https://krita-artists.org/t/make-gmic-window-not-modal-again/68434/3