Obsidian and Bookends workflow

I am using Obsidian for note-taking and Bookends for managing PDFs and referencing. Both work well for me separately, but getting them to work together is a challenge. Currently I mark up a PDF – e.g. a journal article – in Bookends on my iPad, then go to Bookends for MacOS and export notes and annotations in Markdown, which is then opened in Obsidian and given a template for organizing the metadata and notes. It is the latter bit that is so time-consuming and creates the most friction. Has anyone a shortcut or script that would make this smoother?