Well, to me, caching the files and then zipping them for download doesn’t really seem to be worth the effort. You’d have to write and test the code. And the already mentioned added overhead of unpacking the thing afterwards adds another friction to the workflow.
A communication with a possible Obsidian plugin actually appears to make more sense to me. But don’t rush that. Let the API settle in first. Later maybe one could ponder over a dedicated Obsidian web clipper perhaps similar to the one coming with DevonThink. That would offer a total different range of possibilities.
So far, after having played with your web clipper and Obsidian for a while now, I will say, the workflow is pretty good. Having to acknowledge every single file for download creates less friction than initially expected. At this point again thank you for investing your time in this 
I would say, if you find a way for your web clipper to remember the last used directory, that would be the cherry on top.
For anything else or more, I’d look into the possibilities the Obsidian plugin API will offer 