I routinely have manuscripts bounced back by editorial assistants who ask "Why can't I edit your PDF? Can you send me the word source?" Hopefully policies like Elsevier's Your Paper Your Way and the PNAS equivalent, "express submission," will promote a new norm for first submissions.
For my own memory as much as anyone else, here are some tips for getting Elsevier's maddening EES to accept tex source:
- Uploading an archive with all files never has worked for me, so I skip this step
- Use elsarticle.cls and the included model5-names.bst for formatting and APA-style references
- Upload both .bib AND .bbl files as supplementary information (this was the tricky one!) – why would this be necessary?
- Upload all figures separately; PDF format has worked for me though EPS is requested.