The conf/thing, conf/item, etc. folders are only for, as you said, the text file based configuration. Any thing, item, or rule you create in the Main UI is stored instead in the autogenerated json files in the userdata/jsondb folder. They will look very different than the text config files.
If you are thinking about editing them, think carefully and make absolutely sure that is necessary. If you still think you have no better option, then make sure you read through the recent post by @rlkoshak giving excellent directions on how to do this safely: