Having dozens of "references" sections, one at the end of each "subchapter" of the book (article), is extremely uncomfortable to navigate because you never know what page to open. On the other hand, having references as actual footnotes on the PDF page is liable to cause rendering issues.
Cristoph thinks the best is to group all references at the end of the book, as PediaPress did in mwlib.rl after a lot of thinking; and he convinced me. :)
More thinking at:
- Reference handling in printed books
- reopened – volker – urgent – major – 13 months