Interesting, I don’t know of any Defold game that has support for custom user content yet, I think it sounds like a cool idea! 
I would suggest that your users create their own levels(?) in for example Tiled and export to an easy-to-parse format like JSON (I believe Tiled can export JSON). You should be able to read the custom “tilemap”/levels using Lua io.* functions, and parse the JSON data into Lua tables using Defolds json module.
Then internally in your game you setup an empty tilemap that you at runtime can modify based on the custom user level data.
I don’t think there is any need to use either bundle_resources or custom_resources since with the io.* functions you can read files from anywhere.