I don’t have time to test right now, but, I have seen a lot of posts on .Site.Pages vs .Site.RegularPages in here, so, you might search for that. Or, ask the theme author.
I looked at your source earlier and have a comment. You can override by making the same files as the theme, but a level up in the repo. The point being, you can commit those changes without it being troublesome, since the theme is often just fetched from git.
I wrote the theme in question and it worked a year ago. I really don’t know what changed. The .Site.Pages variable just doesn’t contain the pages from the posts directory, even though hugo does render the individual pages.
I have also tried a couple other themes from troubleshooting purposes and I get the same results.
I was able to fix it. I started from scratch, adding parts of the repo to the new site in little pieces, until I had the whole thing working.
I wish I could report back exactly what the problem was, but I still really don’t know. Even after comparing the differences between the working version and the non-working version, I couldn’t figure it out. Perhaps it’s because there are so many permutations of template precedence that I don’t always know which files hugo is using to generate a given file.
What I do think is that I must have had something messed up somewhere and hugo was silently choking on it. Would have been nice to get an error message.
Along the way, I refactored to use baseof as you suggested, and that is cleaner.