Whether the files are still there, or whatever - that doesn’t matter to me. What matters is that it works properly. With notifications for updates going through Discover. Clicking on that notification loads up Discover. And when Discover loads, it has its own icon and not the Bazaar icon (whoever had the idea to do this - I dunno what was going on in their head).
Does Aurora have some GNOME applications in it already? Sure. That’s fine. But this isn’t some extra application. Or some clickable “default application” selection inside settings. This is the entire software center. With its notifications, desktop search integration, etc… It’s already there, and a part of KDE.
I get why Bluefin would switch it out. GNOME Software Center is slow, clunky, and has weird refresh issues when searching. Exchanging it for a new option (that is also GTK and integrates well into the desktop) seems fine. Even Bazzite I kinda understand since it is only incidentally a KDE spin. It’s primarily about the best performance and features for gaming, and geared for newcomers. Fine.
But Aurora? The KDE alternative to Bluefin? Why is it in HERE?
And of course it’s on Flathub. I think it was on their wishlist for a while, but even if it hadn’t been it’s so obvious that it would be on Flathub eventually. 
I only got into this thing when my Aurora desktop suddenly was switched to Bazaar on an update and I was getting double notifications and stuff. Why was this done?
As far as I can tell, the reason to do all this work to remove Discover and try to integrate (as best as the developers can) Bazaar has to do with promoting the Flathub ecosystem. Yes, it is visually discordant with the rest of the DE. Yes, it is missing features (like cancelling an install, or adding/removing flatpak repos). Yes, it definitely has elements of WiP that are not present there in a mature solution like Discover.
However, it’s worth it for the “greater good” of the FlatHub ecosystem. Bazaar allows curated/sponsored applications on the landing page. It directs people to donate money to the application developers. Curation+Monetization. Basically, make it less like a power tool for managing software, and more like, uhhhh, other operating systems’ application stores (fill in the blank here) with big banners and less configuration.
Who knows? Maybe that’s what users want. GNOME Software Center is so clunky it wouldn’t surprise me if the Bluefin users were thrilled with it. But as a replacement for Discover?
I dunno.