PDF's can be annotated with comments and highlights. I believe the data of such annotations are typically stored in the meta data of the PDF file itself. However, there is also a separate format for saving the annotations next to the PDF (https://www.adobe.com/devnet/acrobat/fdftoolkit.html).
The OS application Skim implements something similar and allows you to save annotations as a .skim file (https://skim-app.sourceforge.io/manual/SkimHelp_43.html).
Mendeley also seems to implement separate annotations, as opening the PDF files with a different viewer will not show the annotations (https://www.mendeley.com/guides/desktop/04-read-highlight-annotate). However, it is unclear to me where these annotations live.
Foxit Reader allows the user to import and export annotations as a separate .fdf file, but it requires multiple additional steps and clicks by the user (https://www.foxitsoftware.com/blog/using-comments-data-import-and-export/).
Having a separate annotation file can be helpful for multiple reasons, including working with a Git repository where the PDF's are uploaded once (or even gitignored), while the smaller annotations file is tracked by Git.
Is there software for Windows which allows you to annotate PDF documents and which can by default save these in a separate file and by default load the annotations when opening the PDF?