I'm aware of that.
I'm using quite a few apps that make use of such annoying document package formats. Often I can work around it via symbolic links, for example when using DSP-Quattro for creating DDP masters for audio CDs.
That may work well for a relative novice.
But it's a p.i.t.a. for someone with over 30 years worth of digital archives in a painstakingly maintained Finder hierarchy and structure. We're talking about at least 150 GB worth of documents: layouts, images, photos, you name it. No way I'm gonna move them into an app's "library" package. Apple's Photo.app is already annoying enough in that regard, but at least you can optionally catalog photos without copying them into the library as long as you don't need to sync them via iCloud.
In other words, all I want is a successor to iView/Expression Multimedia – that also did catalog fonts, by the way, although I've never used it as a font cataloger except for a few custom fonts that I've created for clients and thus they ended up in my respective clients' iView catalogs.
I.e., I want to take care of my folder structure myself, because I know precisely what I'm doing. Then I only want the DAM to catalog the files or folders that I tell it to watch, and save just the paths and metadata into its catalog file. Great thing about iView: it doesn't write metadata unless you tell to. Another great thing about iView: AppleScript-able! Its concept was almost perfect for what I've always needed.
NeoFinder is already half way there. But being a DAM never was its primary task, so it will likely never get "there" in full. Yes, I've requested quite a few of such more advanced DAM features already years ago, but they still weren't fully implemented to this day. (Some other CDFinder/NeoFinder features are based on my feature requests, for example the "Support PathFinder" preference check box was my idea… )
And Eagle is in fact already almost there, if it weren't for this library packages requirement. For me that's a 100% dealbreaker. Save the metadata and thumbnails to catalogs but leave my files alone, thankyouverymuch!