Thanks @LucB. This is spot on with Papers 3 and 2020. Unfortunately, the ability to sync PDFs across different devices including tablets is one of my requirement and hence I go down the path of enabling syncing papers3 with dropbox - and lead to the cryptic filename.
The Papers 2020 seems to put everything online, and the Mac native app also feel like a wrapper around the web and not a full-blown desktop app. Perhaps it makes it easier for the sync but nevertheless lack some features such as AppleScript, etc.
Hmm, I will need to think about my PDF reading workflow now. This is the reason I am very interested in Hook, and other knowledge management tools because I haven’t come across a tool that will let me manage my PDFs, annotate (externally) and collect relevant information. I am half way there with PDF reference management (Papers 3), Skim to extract annotations to Markdown (so that the notes can be searchable via Finder), and now Hook helps me to bind everything together! Then Scrivener for writing :). Just need more refinement so that the tools can help me to retain more information in my head and synthesis them better.
Thanks again @LucB.