>  Doesn't seem to work with pdfview yet, and I'm sort of addicted now.

I use pdf-view too (the major mode for viewing PDF files that comes
with pdf-tools, right?) and interleave works great!

> I can think of some changes, e.g., would be nice to keep all my notes for all books/articles/etc. in a single file

Yeah, right now it is one org file per pdf.

> if the interleave options could be set on a per-heading basis that would be really cool.

What sort of options are you thinking about? Right now it creates one
org heading for each set of notes corresponding to a page. 

May be you can work with the interleave.el dev to add in your ideas
and code. I had worked with him to make interleave support pdf-tools
and it was a pleasure to work with him.