Also, when opening on of the popups that feature a new item it briefly flashes very light blue in dark mode.

Thank you, @Sjoerddebruin for reporting it! That change in color when a notifications changes from unseed state to the seen state, seems to be consistent with instances where such colors appear. For example, a success message (for a saved edit) displays the same color:

So, here is an animated gif for notifications displaying the same color when their state is changed (specifically the number four displays a green-blue color):

I don't seem to be able to reproduce any of the issues mentioned in the descriptions on enwiki's Special:Notifications (already on .wmf13). @Etonkovidova can you confirm?

I'm not able to reproduce the issue mentioned here in the comments either, but maybe I'm not understanding it well enough.

In T369591#9972441, @Michael wrote:

I don't seem to be able to reproduce any of the issues mentioned in the descriptions on enwiki's Special:Notifications (already on .wmf13). @Etonkovidova can you confirm?

I'm not able to reproduce the issue mentioned here in the comments either, but maybe I'm not understanding it well enough.

All issues reported in the task have been re-checked and marked as Done in the task description. I closed the task as Resolved.

In T369591#9971327, @Sjoerddebruin wrote:

Also, when opening on of the popups that feature a new item it briefly flashes very light blue in dark mode.

I now stumbled over a way to reproduce this and have created T370042: New Notification flashes bright blue, unreadable in dark mode for it.