We’re glad you like Paperpile. Unfortunately, at the moment there is no way to add line numbers to a Google Doc. This function does not exist. You are actually the first asking for it, so we never thought about whether it’s possible for our plugin to add these numbers. Seems to be tricky but we can look into that.
The only robust option I see at the moment is exporting the document to Word in the end and adding the line numbers there before submission.
Also it would be interesting to know how important the line numbers really are for these journals. Many journals add them to the PDF they create for review automatically these days. The manuscript guidelines are often from a time before PDFs and e-mail and have never been questioned. But it might be field specific and they really matter in your field. I used to write papers in the biomedical field and happily ignored any manuscript guidelines without bad consequences for more than 10 years…