I'm wondering why org-format-latex-options are being overridden here...

[sebeaumont]

https://github.com/emacs-jupyter/jupyter/blob/b279c90295ed7ef89832d655cf8d9077233f1098/jupyter-mime.el#L425

These are a user customisable settings. I know that they are not now fully implemented in org-process-latex but that should change soon.