I hadn't realized that Japan was so similar to Europe technologically. I think you would probably need a less centralized Japan, not necessarily un-unified, but where the daimyos could choose to side with European, and then be annexed themselves.
I'm trusting Iori on this - I know in the period before the Tokugawa, Japan was certainly roughly comparable. It might have ossified as a system a bit by the period you originally mentioned, but the tech isn't static - just underused.
And a question the comes to mind: Why, in particular, would one want to control Japan as a colony?