goodnotes as a windows native app with the created files and folders accessible/managable throu the file explorer.
option to choose where to save the files (saving on another drive for example, switching standart folder would also be useful)

the folders and subfolders created in the app are made in the selcted folder, accessing it via file explorer will give you the exact same strukture

advantages:
-easy selecting of specific files via explorer without the need to exit already opend files (if you need to look something up while working on homework)
-possibillity to share specifi files or complete folders without the need to export as pdf etc.
-better controll over the saved data with good overview
- possibility to save on NAS if desired
- user experience would be the same as on the ipad, just the ones prefering the file explorer would have that option

for still having the "cloud sync" feature the standart folder after installation can be onedrive, so that only the ones who want to use said features can change it.