TSTSNBN, or the third sequence as you said above, to me as always existed as a possibility but not a sure-thing. Meaning that while in concept it exists, Bakker hasn't been 100% sure he would ever get to writing it.
I think 2015/16 will be a big couple years for Bakker, and will probably be a decisive indicator of what he does or doesn't write. With the release of TGO/TUC, possibly as two book, he concludes his original vision. This publication in Grimdark for The Knife of Many Hands also looks like another stab at success. If there is every going to be a sequel to Disciple of the Dog, or an expanded Earwa glossary/encyclopedia, it will be in the next two years. Make or break for Bakker. If he does well and can support himself and his family with the revenues that those publications generate, then I'm sure we'll see him write TSTSNBN and other books. If the next two years are just more of the same, then its not likely he'll be able to continue writing, at least not full time. We might still get more from TSA or other novels, but I'd guess that something as grand as TSA won't ever be finished if its relegated to part-time status.
As for who published what, I'm not overly concerned. Its not like Penguin has been doing great things for him anyway.