Hmm. Not sure what I'm doing that's special but both latex pdfs I produce and others that I read generally work just fine with pypdf, and I really am not adding any flags at all (my makefile says I just go
latexmk --lualatex -aux-directory=output -output-directory=output $<
\usepackage{cmap} is usually what does that:
> The cmap package provides character map tables, which make PDF files generated by pdfLATEX both searchable and copy-able in acrobat reader and other compliant PDF viewers.
(from https://ctan.org/pkg/cmap)
I don't use cmap or pdflatex. Weird.