Sharepoint - 404 HTTP Module causes an authentication popup in Manage Content & Structure page

I have encountered the exact same issue you're having - a HTTP Module that handles 404, and getting 404's (and thus an infinite loop or a 500) when going to Manage Content and Structure.

We also did what you did, and just remove the module for the authoring environment, but another 'short term' workaround until Microsoft sort this, is to put a 1x PNG file with the same filename in the same path that is reporting the error, just to stop it 404'ing.

EDIT: I don't remember /_layouts/none, you might as well just need a //HACK for that. I do believe this is a legitimate bug with SharePoint.