I've been talking to a guy from Amazon Video support about this topic for weeks now. He's been reporting problems on a show by show basis, and much to my surprise, there is genuinely a lot more 5.1 on Amazon now than there was a month or so ago. The Man in the High Castle is an odd one though, and he told me that according to the Amazon app devs, the show does include a 5.1 stream, but there's an issue with the ATV which prevents it from detecting it. They're apparently "looking into it".
Of course there are other issues as well, such as whole app feeling like a sluggish web app and not at all like it belongs on the platform, but I suspect that isn't something that's going to change anytime soon, if ever.
I'd at least like to see video and audio parity with other Amazon platforms, which means Dolby Vision and Dolby Atmos.