Yes, this siloing stops me from using annotation features "native" to each app and format as such as well.

Instead, I prefer to exfiltrate information from the silos(apps, formats, etc) and put them into my note taking system. Then I can do highlights, annotations, etc. on my own terms and also get the benefits of centralization such as searching and linking(the OP has another post describing their own system, which is pretty cool[1]). Currently I'm using Notion, which is also a silo of its own, but it's one that gives me a lot of control over how I lay my information out(and an escape plan from).

There are a lot of perspectives on this issue with data silos and walled gardens. But I'm of the opinion that it's a fairly bad state for all of us "end users". Computers to me are about infinite flexibility and malleability, but ironically the tools we have for annotation and remixing are in practice worse than what we have in the physical world. Reading a book in the physical world, I can converse with the author simply by jotting marginalia with my pencil. It's fluid, intuitive, and the medium of paper encourages it(in fact it can't help but be mutated by my use!: pages get bended, stained, torn, etc.). If I want to go further I can add post-it notes to mark interesting passages, I can xerox some pages and create subsections, if it's a magazine I can just tear them all out! That kind of flexibility just isn't available on a computer.

I think it's worth thinking really hard why we're in this state, especially since computing pioneers were actually very optimistic that data and computing would be way more personally malleable than it is now(I've been working on a small comic on this theme myself[2]). For example, check out this short demo[3] of Smalltalk where Alan Kay hooks up a single frame from an animation of a bouncing ball to a painting program, to modify that one frame while also monitoring the loop. Smarter than paper, but way more flexible.

My own thinking lately has been that developers need to think more about how their apps, like your PDF viewer, could cooperate with other apps to achieve our goals. All sorts of deep questions spring forth from here: "what is the best inter-communication system for them to cooperate with?", "how do you design them to intuitive?", "how can you make the UX as good as 'packaged apps'?". And looking at the history of personal computing, these are fairly old questions. The Unix Philosophy provides us with some clues, and its success, even in the smaller world of developer-oriented computing, gives us some hope.

Personally, I'm excited to one day live in a world where my desktop and smartphone and other devices -my computing spaces- feel less like a collection of walled gardens that refuse to intermingle, and more like one big beautiful garden, an ecosystem: lots of small, useful programs, chatting and cooperating, data freely flowing between them, each new program multiplying their collective potential and creating a new ecology, that I can adapt to my psyche and my needs, helping me be a better human.

[1] https://beepb00p.xyz/pkm-search.html

[2] https://twitter.com/yoshikischmitz/status/118845556004515840...

[3] https://youtu.be/AnrlSqtpOkw?t=607