Hmm, nothing should have changed in this regard. The references to external files, be it external tilesets or images, should be relative whenever possible. The only time it isn’t, is when you’re using Windows and are referring to a file on another drive, because then it is not possible to use a relative path.
I just tested it by saving the example “desert.tmx” map as a JavaScript “desert.js” file and the reference to external “desert.tsx” file was relative like it should be.
If you believe you’ve run into a bug please provide some more information, for example which platform you’re on and where you’re saving the map and where your tilesets are.