This is a well thought out theory, but most of this is just speculation as we have not seen a hyuga battle an EMS Uchiha, but I highly doubt a Byakugan user stands a fraction of a chance against an EMS user.
1. Take a look at all the MS/EMS users we know, they are all pretty much beastly legends, besides Sasuke, but he may as well be on his way there. They are all extremely powerful, and have some of the most hax jutsu in Naruto. I doubt Neji could beat an EMS user.
2. The Byakugan has had virtually no growth since part 1, this is a major drawback because the Sharingan has evolved multiple times and back then Sasuke and Neji were somewhat on equal terms. Not saying that Neji hasn't grown, but his power boosts have not been as significant as the Sharingan has.
I do find this theory very interesting, I have not written it off, because you make some valid points. You used Naruto logic to come up with your conclusions, Example: Neji was able to remove the webs from his body by expelling chakra through his pores, logic would suggest that this would have the same effect on everything that he comes in to contact with, but can we really use logic in Naruto??
Anyway, my final conclusion, I don't think Neji could beat EMS Sasuke, he would just be too much for him. But if we were able to see the full extent of what Neji is capable of now, he would probably have a better chance against an MS Sasuke.
I will give you rep for this though, so, + Rep sir