So, back to the original topic... what all the discussion seems to highlight is that currently there are only two successful means to convince the game to read modded data files: 1. place them in Content\Configuration\, overwriting the original vanilla files; or 2. use a custom scenario and place the modded files within it. The potential third option of placing the files in Content\Mods is broken and doesn't work. Further, it currently ONLY supports modded ECF files and not even a modded Localization file; as a modding system it is insufficient. The method needs to be reworked to better mirror the method that other games have used to support ALL modded game assets. If you wish to avoid using a scenario, it would seem that the ONLY practical method you can use is the method that I used successfully for years and described in detail in an earlier comment. That method can also be extended to the Localization file and other game assets.
It is,just temporary. The very first version of "config files" dates back to late alpha 7.xx, where the Config_example.ecf and config.ecf were the only available files for us to mod. Then in a later version they extended this to some other files in the Configuration folder, adding more over time, up to the point the Config.ecf was somehow "downgraded" and only kept for API mod calls support, but not for general player usage. This left us in murky waters, where only the "modding savvy" players could still manage to keep their changes up to date by transferring them to the other config files. The Config.ecf had the advantage of allowing modding of blocks/ items directly from the main game folder without affecting the content of the other files, so the "Mods" folder was not even required at that point. But there are some other options that Eleon can look into to allow modding the main game without forcing the players to transfer it all into a custom scenario, and without affecting the main game files either. Like you wrote, the "Mods" folder still does not allow custom stamps, models or Localization.csv or anything other than the files in the \Configuration folder.