That makes sense, I followed your guide on githubon the main screen pressing left or right will change to external storage if present, if nothing happens, then FDD is not enabled in your settings. Also keep in mind the ini is saved into the savedata, and changing ini will not do anything. you will need to export the save using JKSV, delete 'SaveData00088000.bin' and restore for the system to recreate the settings using ini again. Sorry if my explaination is not very clear.
Floppy was disabled in my ini for FDD.bin, now it's enabled I see panels for side 0 and side 1 of the floppy.
I put a test save game in there that I found online from Sonic R and it shows up. But as you say I cannot copy anything into the floppy without getting a Switch UI error.