Here's an interesting thing, which is further evidence that the problem - or misconfiguration/our misunderstanding - relates to sizing that happens before Color:
1. Put the 1080p PNG sequence on a UHD timeline.
2. On the clip on the timeline, in the Inspector set Retime & Scaling -> Scaling: to Crop. This will display it at 1080p resolution, ie not scaled up.
3. Go to Color, apply the Motion Blur.
4. Currently there are no artefacts, because no scaling is occurring
5. On Color, go to Input Sizing and set Zoom to 2.0. The artefacts re-appear, as expected - this is exactly like scaling on the Timeline
6. Set Input Sizing -> Zoom to 1.0 again. Now change to Output Sizing and set Zoom to 2.0. Boom, no artefacts!
So first of all, this gives us a second solution/workaround: you could not use Super Scale, and instead do the upscaling using Colour -> Output Sizing.
Secondly, why does this work? It suggests to me that when scaling is applied to footage with an alpha channel before it reaches Color, artefacts occur when effects alter the alpha channel, ie Motion Blur. However, when Color is able to apply those effects first, then scale up the result, no problems occur.
Is this a bug? I really don't know. If it is a bug it seems like a serious one, that I'd think someone would have noticed and talked about already. So I'm still wondering if we're doing something wrong here, or misunderstanding something. Or maybe this source image sequence is unusual. Or maybe it's related to PNG. I'm not sure.
More testing is probably required, unless a Color page expert can chip in.
In the meantime you should have two solutions / workarounds:1. Enable Super Scale in Clip Attributes
or
2. Don't enable Super Scale, and instead don't scale on the Timeline (Rescale = Crop) and do your scaling using Color -> Output Sizing, which is applied after your Color page effects have manipulated the clip.
EDIT: I've just realised that Output Scaling applies to every clip on the timeline. So this is only a workaround if every clip can be scaled the same way. If you need to scale different clips differently, or some not at all, using Output Sizing probably won't be usable as a workaround for the alpha issue.