This is a bug that applies to Generators created in FCP X and Motion, exported as ProRes4444 and then imported into either Premiere Pro or After Effects.
Either in FCP X or Motion, create a project that starts from the first frame with a generator such as a Color Solid (it must be one with a fully opaque alpha channel, so for example the Motion Caustics Generator which has transparency doesn't behave this way). Don't scale it down or crop it or mask it - it must be full frame.
Cut the generator so that it doesn't run for the full length of the project, in other words so that there is transparency after that point.
Export as ProRes4444 and import the result into either Premiere or After Effects.
You will find that the section of the clip that is meant to have transparency does not have any and appears black rather than see-through. Interpret Footage reports the clip as having no alpha channel in the sense that the alpha options are greyed out.
Importing into anything other than these two hosts (including of course the Apple applications) seems not to exhibit this problem.
in other words, something written into the ProRes4444 header is overwriting the alpha channel for the duration of the clip in such as way as to confuse Pr/Ae.