I've been developing a more elaborate variation on the "chat with a pdf" idea for my own use as a researcher. It's mostly designed for a historian's workflow but it works pretty well for science and engineering papers too. Currently Flash 2.0 is the default but you can select other models to use to analyze pdfs and other text through various "lenses" ranging from a simple summary to text highlighting to extracting organized data as a .csv file:

https://source-lens.vercel.app

(Note: this is not at all a production ready app, it's just something I've been making for myself, though I'm also now sharing it with my students to see how they use it. If anyone reads this and is interested in collaborating, let me know).

I'm building such tools at https://sugaku.net, right now there's chatting with a paper and browsing similar papers. Generally arXiv and other repositories want you to link to them and not embed their papers, which makes it hard to build inline reading tools, but it's on my roadmap to support that for uploaded papers. Would love to hear if you have some feature requests there