Latest versions don't use Cloud Save anymore. They've been changed to Cross Progression.
https://support.cdprojektred.com/en/witcher-3/nintendo-switch/sp-technical/issue/2431/how-to-use-cross-progression-2#:~:text=Make%20sure%20your%20version%20of,will%20be%20enabled%20by%20default.
Hi, I've actually found out why the main menu is different. It seems like you forgot to convert the tga textures to tpc, so the mod textures get overridden by the original textures.