Wierd thing with Transmission on Coreelec, my custome settings.json file is overwriten every time I start transmission
I use the following path /storage/.kodi/userdata/addon_data/service.transmission/settings.json
Only the settings available through the the settings of the transmission add-on are overwritten.
Use the settings of the transmission add-on to set them.
If you still have issues, provide more details here.