Yes, you read that headline correctly: for JGR Space Physics, and I think any AGU journal, the initial submission of a manuscript can be in any reasonable format. As long as the paper has all of the essential elements (title, authors, abstract, main body, affiliations, references), it will be passed on by AGU HQ staff to the editors for consideration. We really like line numbers, too, as that greatly helps the editor and reviewers comment on specific text within the manuscript.
What does this mean for you as an author? It means that if you usually submit to a different journal, for example Annales Geophysicae or ApJ, and you prefer to prepare your manuscripts in that journal’s style format, then please, by all means, do it. Even if you intend to (or eventually) submit it to JGR Space Physics, you can feel free to prepare and submit the initial version in another journal’s formatting and referencing style.
So, here is some advice:
I don’t care which style guide you pick, at least for the first submission of a manuscript.
If it is not declined for publication, then for the second submission of the manuscript, it will have to be converted to comply with AGU formatting standards. This is the point at which publication is becoming much more likely and we need you to make it ready for the production staff.
Note that the second submission is also the point at which you need to upload the figures as individual files. For the first submission, this is not required. A single PDF of the manuscript, with figures either embedded throughout the text or clustered at the end of the document, is all that you need to upload.
Finally, for any submission version number, you can replace the GEMS-generated PDF with your own PDF. I find this especially helpful for the resubmissions when the figures have to be uploaded individually. GEMS does not annotate the figures and therefore they are unlabeled and not numbered, with either figure numbers or page numbers, in the GEMS-generated PDF. Uploading your own version of this PDF, with the figures numbered and paginated and perhaps even embedded within the main text, is not only allowed but also beneficial and appreciated.
We hope that this makes it more convenient for everyone to submit papers to AGU journals. I think that this loosening of the initial submission rules will most directly help those who only usually published in other journals and occasionally publish in JGR Space Physics.