In Espens Aarseth's article Playing Research he points to this problem when saying: "Konzack’s method is probably best used as an open framework, where the analyst can choose any 2-4 of the seven layers to work with, and ignore the rest. Furthermore, layers should not be seen in isolation, but probably analysed together for best effect." (p. 2)
I could not agree more. In fact, rereading the paper Computer Game Criticism once again, I would like to amphasize the end part of the paper in which I'm saying: "Each of these layers may be analysed individually, and we might only analyse one or a few of these layers. However, the other layers still exist and influence the true nature of the computer game." (p. 99)
It is important for the game analyst to discuss which layers s/he would like to include and what layers are more or less excluded from the analysis. The question of why some layers are included while others are excluded is of course crucial to discuss openly. Otherwise the reader might become puzzled.
Keep in mind, it's ok for the analyst to admit s/he can't adress all issues and every angles of computer game analyses in one essay or project. By focusing on only a few layers s/he will be able to work in one direction towards the conclusion as the final outcome of the essay or project.