To date, you are the only other person I've seen try to morph videos like that. It's tough! I find that no 2 flights are exactly the same. To fix this, because I'm shooting in 4K, I can digitally zoom each track about 10%, which gives me some wiggle room in post to better align the not-perfectly-aligned videos. Even then, "perfect alignment" is the Holy Grail.
I've applied your same principles to this construction video:
I call this "test video" because I haven't color corrected or anything like that. This was done in Sony Vegas Pro 13, which I'm dissatisfied with. I now edit in Adobe Premiere Pro (which I'm still learning), and am going to revisit this project.
This construction project completed about 2 months ago, so I have roughly 8 more shoots to add to the final video.
Like you, I have also sped up the video (4x). Unlike you, I have been using Autopilot. I like Autopilot, but it DOES have its issues. For one, if I'm not careful, it will overheat my iPad Air Pro. If it's hotter than 80° outside, I have to keep the iPad in a cooler with some ice until it's ready to fly. And then I have to make sure the iPad stays in the shade. It can be maddening, but I kind of have it down to a science.
Good job on your videos.
D