I can totally relate to all of that. My current approach to it is to fill in the gaps in browsers using other tools. Minimize dependence on both tabs and bookmarks since they suck so much. An editor containing my notes open next to the browser. Making copies of things I care about (and giving them good backups) as it's become clear that we can't depend on anything to last out in the world.
I've actually started to think that this kind of hodge-podge of tools is a good thing. Software is hard, bugs are inevitable. Multiple tools from different authors make my setup more resilient. Tools keep growing more complex; adding features to a single tool only exacerbates that trend. I also feel a greater sense of agency. I'm not at the mercy of my tool provider, I can identify problems and solve them for myself.
Multiple tools from multiple people make it less likely that the entire ecosystem is going to collapse, but makes it likelier that any one tool will stop working.
But that's not even my main problem. Integration is. Integration consolidates ideas in ways that can be packaged and spread to others, increasing the mind share of the paradigm. Unless a good solution is integrated, it will be the domain of a few hardcore adherents. Once an integrated solution appears, it will become resilient only by the virtue of being popular and cared about (I guess as long as it's free software).
The flip side is that a modern web browser integrates so many things not core to any data management idea that few dare experiment with it.
I'm curious about the Arc browser, but I won't bet my workflows on it unless it becomes open source.
I've actually started to think that this kind of hodge-podge of tools is a good thing. Software is hard, bugs are inevitable. Multiple tools from different authors make my setup more resilient. Tools keep growing more complex; adding features to a single tool only exacerbates that trend. I also feel a greater sense of agency. I'm not at the mercy of my tool provider, I can identify problems and solve them for myself.