LivePano -a way to do this without using PanoTour pro - AutopanoGiga ?

By using the video player plugin and adding the video as panoramic image code to your XML.

<plugin name="video"
        url.flash="videoplayer.swf"
        url.html5="videoplayer.js"
        videourl="video.m4v|video.webm"
        posterurl="videoposter.jpg"
        panovideo="true"
        pausedonstart="false"
        loop="false"
        volume="1.0"
        onvideoready=""
        onvideoplay=""
        onvideopaused=""
        onvideocomplete=""
        onerror=""
        />


<image hfov="360" vfov="180">
   <sphere url="plugin:video" />
</image>

https://krpano.com/plugins/videoplayer/

Partial pano's are supported for pano's that are single-res, not multi-res.

I'm not sure for video. Give it a try.

Hmm yeah that is interesting.
After reading some more, I suspect you might be able to replicate the Panotour way by doing the same or similar to what you suggested: adding a partial video sphere as a distorted hotspot and lining it up with the pano perfectly, but I'm out of my depth here. I'm not a photographer, just a web developer.
Interested to learn more.

When you take a pano, is the ath set to 0 at the beginning point of when the panorama was taken? If it is, maybe you could simply take the video at the exact same position just before you take the pano, and then set the ath and (maybe) atv to 0 and it would seamlessly line up with the pano.