The exact problem with Web.config modules is that they are never handled in your code, only in the config. It also is very IIS-specific, precluding it from working easily with other web servers cross-platform. With OWIN, by starting with code, there is nothing stopping you or someone else from making a config-file-driven middleware loader to accomplish the functionality you're looking for. i.e. app.LoadMiddlewareFromConfig("middleware.json")
The only thing that precludes Web.config from working cross-platform is the absence of reliable implementation of a cross-platform web server. For example, I don't even consider Nginx reliable on Windows; some nasty effects are in place. The best home for Nginx is Linux. The best home for IIS is Windows. Cross-platform sounds sweet in theory but in reality it goes down hill pretty fast with subtle defects.
