Chrome Version: 53.0.2785.101 (Official Build) m (32-bit)
OS Version: 6.1 (Windows 7, Windows Server 2008 R2)

Following the resolution of  bug 237873 , Chromium allows individual users to install native messaging host applications for themselves without having to elevate their privileges. On POSIX systems, Chromium looks for user-installed NMH manifest files in the "NativeMessagingHosts" subdirectory of the user data directory Chromium is currently using; on Windows, it looks for subkeys of HKCU\SOFTWARE\Google\Chrome\NativeMessagingHosts\ in the registry that point to manifest files.

A downside of looking in the registry for paths to NMH manifests is that all Chromium processes running on a Windows system under a particular user account will find the same set of NMH manifests; unlike on a Linux/OS X system, it's not possible to contain a NMH manifest to a single Chromium process (e.g. by starting it with "chrome --user-data-dir=[temp_path]" and placing the NMH manifest at [temp_path]\NativeMessagingHosts\[whatever].json).

Would it be possible to make Chromium also look for NMH manifests in [userdir]\NativeMessagingHosts\ on Windows, like it does on other OSes? This shouldn't be a security risk: regular users can already write their own keys under HKCU in the registry without privilege elevation, so this is no more risky than the way Chromium already implements this feature on Windows.