Thoradia add-ons store their settings in their respective home directory, which is accessible via the userdata network share.
Transmission therefore stores its settings in /storage/.kodi/userdata/addon_data/service.transmission, accessible via userdata/addon_data/service.transmission.
The underlying applications are installed with their respective default settings, that you can customize.
Add-on updates will not affect customized settings.
Safest is to have only one Transmission add-on active.
Which one you keep is up to you.