I used Tiled to design the levels in Depth of Extinction! Really love your product for making levels in Unity (and the Tiled2Unity plugin of course).
What's the benefit if I already have tiled2unity set up? I actually use tiled2unity Lite as I am on a Mac and just prefer it since it removes the intermediate application as well.
Right now there would not be any big difference, what I did was to move all the importing process into Unity instead of having an external tool like tiled2unity or tiled2unity Lite, so Unity Editor takes the TMX file an does all the process that tiled2unity used to do externaly. There is still an XML file generated by tiled2unity, that's my next objective to remove that file then you would always have only your tmx file in the unity project. In my opinion the usage of TMX file inside Unity would be more clear an transparent since the workflow would be very similar to importing a FBX file for a 3d model.