I found a way to save core options in iOS Retroarch.
Make sure you have previously ran two games from separate cores so they show up in your history. Load up one game and change the core options. Now go to your history and load another game with a different core. This effectively closes that core and saves the options.
To add to this I found out you can also select the first option in the core options “Manage Core Settings” and save it manually.
Yes this seems to help a lot to save pUAE defaults for Amiga WHD settings so thank you for this… although I still can’t quite get Amiga to work (yellow/black flashing screen)
With Amiga I can only get zip files with disks inside to load.