I use Scrivener a lot. And Scrivener has this feature called “collections”. You can use this to combine your notes into one collection without changing the actual structure of anything else. English is not my first language so I struggle a bit to explain it. But it’s basically like bookmarks for your own documents which you can organize however you want.
I know that I can use embed searches. Which is somewhat similar but not exactly what I want. What I would prefer is the option to create folders where I can put some notes, without moving the actual files. So that I can put one note in multiple folders, if I want to. Like virtual folders which I can browse in the fileexplorer like my normal file structure.
I’m just starting with Obsidian, but from your description, it sounds like tags would be the easiest solution (and you can have both the file explorer and the tag pane open at the same time) …