I understand your desire for a nice iBooks-like app that feels like a single item you can just click, but wondered whether it is possible to package this up as something that puts the html files somewhere on the ipad and a command that opens your browser pointing at the index page? But I guess you would rather just have one big file, like a PDF.
Now that you mention it, it is indeed a bit pointless to just make the html files locally because you can download the zip of them.
When I did the “make pdf”, it did not make a pdf file, as you noted. After you make it, I think it printed instructions to change into the build/latex folder and run make there, which runs latexmk to make the pdf. You have to have installed latex. I did this on MacOS and Linux and neither worked for me (as I reported above). On MacOS there was a problem finding a font. On Linux, it printed some weird conversion errors. With enough energy I could track down and fix these problems on my machines, but I don’t have the energy to do that right now.