There are three problems noted here, however only one is a bug.
The bug is the disappearing bodies. This is logged now, so thanks very much for the example. (internal reference FUS-29023)
There is a workaround. Just select the Tool Bodies first, prior to picking the Target Body. There should be no visibility issues with that workflow.
The other two items you mention are expected. As @hanvota points out. (thanks!)
The stripes are the preview of the new component you are making. Because the Hull is the target body, it's body is being copied into the new component, and the preview of the overlapping bodies has stripes. One could argue it's a bug because it's unexpected, but to me it's a helpful guide to ensure I'm getting two Hulls as I work. IMO it's valuable feedback. If it is more than that for you, please let us know how, we value your opinion.
The section analysis showing two shades of blue on separate parts might be a fluke, if the same color was used twice. There are only so many shades used by the section analysis tool. The other possibility is that it's related to the new component preview of the new component with the existing Hull component edges superimposed on it. It's hard to tell from your video. If you close the file and re-open it does it still show blue on both components? If you turn off the original Hull does it look better?
In my testing I reliably got different colors on either side of that line between the flanges, so I'm not sure here.
If you have more questions, feel free to ask.
Thanks,
Phil Eichmiller
Software Engineer
Quality Assurance
Autodesk, Inc.