Sure, but the vacuum belonging to a theory must be part of that particular theory. I really do not see where the paper develops the "stuff" (for want of a better word) from which anything self organizes. One cannot discuss self organizing without in some way, defining what it is that is self organizing, what it's properties are, etc. The author's aims are not to go beyond qft, but to replace it, given that the thrust is that quantization isn't fundamental. In qft, quantization is fundamental.For the vacuum this proliferation of models has already occurred, i.e. the vacuum isn't a unique feature of QFT anymore; any theory aiming to go beyond QFT has to describe the vacuum as part of nature; how it does so depends on the underlying mathematics.