For what it's worth I got pretty decent conversion results of one file at a time with the Ubuntu repository version (0.9.9)
But that version doesn't work with collecting it into a single output file, no.
I think it was a mistake to try shaving off a couple of lines and a step at the price of a more convoluted install and a brittle process.
Most people would probably be best off just converting one HTML file at a time to pdf (e.g. pdfkit.from_file(filename_in_html,filename_in_html[:-4]+".pdf") in some sort of iteration over the file names) and then concatenating the resulting PDF:s, for instance from command line by