Is it possible to say, take a mod like this one here: http://community.playstarbound.com/threads/a-less-yellow-stardew-updated-7-3-2016.116225/ which, has a LOT of .xnb files it uses as replacements to create the new environment, and just place it in the folder of the mod, which goes in the "Mods" folder, and then just have the game use the modified versions when it needs them? Instead of manually replacing all the .xnb files and making a ton of backups... so when the game needs a file, it'll call the file that's in the mod folder instead of the one that's somewhere in the "Content" folder.
That is possible to do yes, you would have to use EntoFramework to make it so, but yes, completely possible (It is how SeasonalHouse - soon SeasonalBuildings - works)