As far as I can tell (from my initial reading), the author (and many many commenters here) seem(s) to be confusing polynomial time (P) with polynomial circuit size (P/poly). These are completely different complexity classes in style and probably in power, too. Last time I checked, there was not a good characterization of P in terms of circuit complexity (the attempt at doing so is P/poly). So, logically, comparing P and NP is not even possible without additional knowledge about P. The exception to this being showing that X != NP where P <= X <= NP.
For reference: P <= BPP <= NP
We know that BPP (a randomized version of P) is (non-strictly) contained in P/poly. We also know that proving P = BPP (which is conjectured to be true by most) requires these classes require superpolynomial lower bounds for Boolean|Arithmetic circuit size. As far as I know, proving an exponential lower bound for an NP-complete problem doesn't immediately rule that P != NP since P !=> only polynomial size circuit size (the circuit size only relates to the size of the advice function). P might not contain problems that require exponential circuit size, but this fact is not stated, proven, nor reference by the author here.
Simply put: The author assumes that P != NP follows immediately from Theorem 6.1. This is not as obvious as they might think it is; many additional details are needed.
Admittedly, I have not rigorously studied or concluded anything from the flattening process the author proposes. I honestly don't believe I have to. Skimming over it, I don't see any way that P is characterized in terms of polynomial circuit sizes (which probably is an assumption as powerful as P!=NP) here. I also do not see any mention of P/poly, which I believe the author is attempting to use.
For a paper approaching the P vs NP issue using circuit complexity, I would expect this much. Because of the lack of even a mention of BPP, P/poly, and others, I would be highly surprised if many of these results in the paper hold at all. Though, hopefully, I might be wrong.
EDIT: Accidentally used circuit depth when I was really thinking of size.