I could be misremembering, but I believe he had mentioned he didn't know what to do with her if she wasn't in a relationship, and since he didn't want to write them together at that time, that is why she disappeared for most of it after Big Time. And might also be why he assumed Bendis would've felt the same way.
I am surprised to hear he did give an explanation regarding Go Down Swinging, because that was one of the biggest question marks for me and I never saw any comment from him beforehand talking about it. It's hard to tell exactly whether those scenes were added in because he knew what would happen in Spencer's first issue, or had to be changed because he was originally gonna end the story with them together. I wanna say the former, just because the transition between 796 and 797 is SO jarring.