Mod packages have been a thing long before Steam Workshop existed and long before Unity/Unreal. Steam didn't invent modding.
And if mod support for non-Steam games was as technically challenging as you suppose, Valve wouldn't need to be sending cease and desist letters to community projects that redistributed mod files. Valve wouldn't need to be verifying purchases before allowing users to download files.
The fact that Valve is putting additional technical and even legal barriers in front of mod redistribution means that it's not just that the mods wouldn't work without a special Steam build. The reality is that many of the mods would work, and that is precisely what Valve is trying to prevent. Tools that allowed for loading mods from Steam Workshop weren't shut down because they didn't work, they were shut down because they did work.
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There's a somewhat weird deference here to technical issues, but it's not clear whether you're claiming that developers are solving those issues or Valve is.
Saying that Workshop needs to deliver assets in the "engine's own format" is really just another way of saying "different games need to be modded differently." But that has always been the case and yet before Steam Workshop modding files were distributed and installed manually. Similarly, asset patching and replacement for games has always been a thing. And mods worked.
To the extent that mods today are drag-and-drop, they are drag and drop because the developers put in the work. Valve is not going into engine source code, decompiling everything, and then figuring out how to get the mod to work. They're providing APIs and mechanisms for developers to tell Steam Workshop how to modify the game files.
So unsurprisingly, the majority of mods that work in Steam work outside of Steam because once the developer puts in the work to build a modding system that's compatible with the assets and files that Steam workshop downloads and once those assets are patched for a version of the game, then developers are shipping that same version of the game on multiple platforms (unless they're using proprietary Steam APIs, in which case it's probably a Steam-exclusive game anyway).
Whatever APIs Steam is providing for Steam Workshop, there is no reason those APIs need to be restricted to Steam. A debundled service could provide the same stitching and the same APIs on-demand for games outside of Steam.
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Now, if you wanted to defend some of Valve's other anticompetitive behavior, such as precompiling shader caches, that would be much easier for you to do, since shader caches are not only game-version specific, they are also often platform-specific, and there's very little way for Valve to provide those assets without knowing exactly what version of the game is installed where. It's not like Valve can compute a single set of shaders and then just give them to everyone, they're dependent on the actual install.
But mods aren't in that position. Developers are putting in the work to support modding, games have to opt-into this system anyway so it's not like 3rd-party installs can't report to Steam Workshop what version they are, it's not like games who are adding modding support can't upload resource files to a debundled Workshop to be modified. And the end result of that process would work for games outside of Steam, as evidenced by the fact that in the instances where you can download mods from Steam Workshop and get access to the files, they tend to work in versions of the game from alternate storefronts.
This is another way of re-saying -- if this was actually a technical issue, Valve would not need to put barriers in place keeping people from downloading mods outside of Steam. If it's so impossible for Valve to support mods outside of Steam, then fine, they don't have to do anything. Just get rid of the extra barriers they've constructed and let communities solve the problem for them without interference. But Valve isn't willing to do that. The reason Steam Workshop has such poor support outside of Steam isn't because it's an impossible technical problem, it's because Valve is taking active steps to prevent people from accessing those mods. Valve could do literally nothing to support Workshop access outside of Steam and the situation would be better than it is today.