Calibre having its own trash folder got in the way of how I use it. I only use it for updating metadata, covers, and format conversion. The vast majority of what it can do I never touch.
After I'm done with some books, I open the library folder, use Agent Ransack (because Windows refuses to allow its own Search to work in parts of where Calibre's default library location is) to find all *.azw3 files then I copy and paste from there to folders on two different storage devices and books I'll be reading soon I copy to the Kindle folder in internal storage on my phone. Then in Calibre I delete everything and only when I have some more books do I use it again.
That's how I've done my ebooks on many devices since 2004, with various software.
But with Calibre hanging onto everything, Agent Ransack would find all the "deleted" AZW3 files too.
Any time any software author adds what they think is an awesome new feature, they should also add an option to disable it because it's a near certainty some people are just going to flat out hate it forever.