I'm suggesting that the mod setup be shifted from cloud to local storage. I understand that it would require individuals to have the same mods downloaded to avoid disruption but with steam allowing for collections, this is not an issue. Most games behave this way. You can add the mods you want to a steam collection and someone wanting to play with you can simply click the "Subscribe to All" button. Shifting to local storage also reduces the issues with content becoming randomly unavailable due to reliance on 3rd party hosting.

Organization-wise, mods should be stored in their own sub-folders with each containing their own "Images", "Models", and "Asset Bundles"... the way 99% of the rest of the games handle it.

This all allows for longevity of content since it would be hosted by steam and then downloaded to each individual machine. Continuing to process mods as is will cause a tremendous amount of problems and headaches for the end-user down the road.

A sort of representation of what I'm proposing:
> Tabletop Simulator
    > Mods
        > My Custom Mod
            > Asset Bundles
            > Images
            > Models