My original post that you linked was specific to note-taking, but in essence your concern is just as applicable too in my own workflow. I struggled to find a system that allows the collecting of various media, not just text. I think I have settled on DEVONThink as the database. I have DTTG and work exclusive on Apple devices so not much issue there. I flirted with Notion.so, but it is too underdeveloped for the features I would use (and basically requires internet to be at all useful).
As I am sure you know, DEVONThink can hold any kind of media so the next dilemma as you pointed out is the notes part. I plan on just creating linked notes to these other media (though I may toy with DEVONThink’s native “notes” field) and hold them as separate files. In this way I can just reference/review/reflect on the note and not necessarily the other media.
Regarding the problem of dealing with annotations, etc, the only way I see out of this dilemma is discipline to go the next step towards creating the ‘usable’ elements of a graphical media in the form of text. As a historian this is something that is essential to my workflow. I may have 100’s of citations in a piece of writing and it is just foolish to think I can be productive if I don’t extract the usable evidence from a piece of media and then ignore the original source until necessary.
For my lecture notes (second brain) mentioned in my original post. I will be curating a kind of abridged version of my research notes with a chain of internal links back to the original source if necessary.
So in essence, its still all plain text, but with reference to the graphical media.