Kimstacks,
First, I apologize for taking so long to reply. I was not monitoring this forum, but I expected to be notified by email of replies like yours. Either I missed the email, or it never came.
Second, I’m only now rolling up my sleeves and learning to use Obsidian in depth. So take what I say with a grain of salt. Nonetheless, my answer to your question is an emphatic NO!
tl;dr Don’t store files with generic file types in application-specific locations unless the application organizes and maintains these files in an intuitive, transparent way for general access by any other application that might be used to work with them.
Here’s why. Certain file formats are designed to be “open,” which means various different programs can use the same file format. The *.md files Obsidian uses are an example. Other formats are “proprietary,” and typically can be used only by the owner of the format or one of their licensees. Adobe originally developed the PDF format, but released it as an open standard in 2008. This is why so many applications, including open-source applications, can now create, access, and otherwise use PDF files.
As a general rule of thumb for organizing open- or generic-format files, I try to store them where I can logically find them. E.g., research-related files are stored in ~/Documents/Research/*. If multiple application programs can use a particular file type, I either keep this type of file in folder(s) dedicated to a specific purpose and/or a general, application-agnostic folder . For example, I keep PDF files of my tax returns in “~/Documents/Personal/Financial/Taxes,” but I store all scholarly PDF files on my (mounted) NAS drive in myNAS/mnt/Volume1/Documents/ZoteroLibrary.
At first glance the folder name “ZoteroLibrary” might seem to contradict what I said about application-agnostic folders. But I use the Zotfile Zotero plug-in to maintain the library, and the plugin names the files according to a user-specified convention (e.g., “Author Date - Title”) and then simply uses the native file system to organize the PDF files. Any other app can find and open the file by simply following the appropriate path, e.g.: “myNAS/mnt/Volume1/Documents/ZoteroLibrary/AdamsP/AdamsP 1998 - Network topologies and virtual place.pdf”. To access the file one could either know its absolute path or (using Finder, shell commands, or another file navigator) navigate to the folder and access the file.
Zotero & Zotfile organize my PDF files in a logical structure that can readily be used by any app that can read PDF files. This includes Obsidian. But Obsidian’s file organization is designed for note-taking, not library maintenance. Anyone using Obsidian’s vault structure would have to know details about what and how Obsidian does things. IMO, it’s best to avoid such application-specific conventions unless they are what ordinary humans would ordinarily do anyway.