I think the point is that we didn’t have to deploy any binary components before to be able to talk to third-party applications already present on the user’s system (or at least launch them).
Due to the security restrictions in WebExtensions, we are not only forced to provide a custom binary for the same use case, but also talk the users into installing an installer from a source they don’t really know. Seems like a bad trade-off in terms of the user’s security.
So, the perfect thing for this use case would be not having to write and deploy any binary components at all and to be able to talk to normal third-party applications directly. I understand that this would put some responsibility back in Mozilla’s hands, but I think it would be a good thing for the user (and the extension developer). The user would still take most responsibility by accepting the “nativeMessaging” permission.