Making an isometric game is not as straightforward, but can definitely be done. As Defold does not support isometric tilemaps, one has to improvise. By far the most comfortable way of creating isometric maps that I have found is to use Tiled map editor, which includes support for them by default. The only caveat is that you have to use multiple tilesets with different offsets to achieve the height difference.
Once your map is done, you can export it into a myriad of formats. I recommend using the .lua file, because you don’t have to deserialize it, which may or may not (?) have an effect on performance. Then it is all a matter of writing your own rendering routine. I am using a custom one for rendering tiles dynamically depending on current camera position. I would like to open-source it as people asked about it, however the current version is far too messy for eyes of the public.
Please check out my thesis, you may find some useful info in chapters 3 and 6.