First off, referring to 'civilizations' as basic entities or units of analysis is just nonsense. Sure, there has been some talk about 'social complexity' up to the mid-90s, but (a) that discourse is largely outdated since it tends to be based on justifying prior presumptions regarding the nature and boundaries of societies that were already assumed to be 'civilizations' without adequate reason, (b) that perspective is being replaced by more bottom-up approaches that model various kinds of behaviours and interactions, including possibilities and limits thereof, and as guided by the archaeological evidence, and (c) even when we do talk about so-called 'civilizations', that is typically limited to a period starting around 4000 BCE. You are clearly ignoring (what I consider to be) the most exciting topic of archaeological research, the pre-pottery neolithic. As bildung points out, coherent models about this period have been formulated by drawing on evidence accumulated from dozens of PPN sites.
EDIT: Beyond the Ubaid is a fantastic edited volume that touches on this shift, with papers by leading archaeologists: https://oi.uchicago.edu/research/publications/saoc/saoc-63-b...
EDIT2: See also: https://doi.org/10.15184/aqy.2014.44 and https://link.springer.com/article/10.1007/s10963-007-9008-1
Yes, it is true that Gobekli Tepe has no habitation associated with it, but we do not consider this an unresolved puzzle. Gobleki Tepe is commonly accepted as a great example of the ingenuity of nomadic peoples. Why do you assume that it would be necessary for its builders to have been sedentary?