Where are my folders in the project? All I see is the assets folder

You have to navigate into the assets folder (in your file explorer.) If you do so, you will see your scene folder, just like your editor (along with some metadata.) The other parent directories are abstracted from us into editor settings, debugging, ect. If you want to add folders directly to your project, you can drag them straight into unity, right next to your scene folder. (Pro-tip, if you hold ctrl before letting go, it duplicates the whole folder.) The reason there is nothing there, is because you have to bring your project to life :) (the best part.)

Well, this is how Unity has always worked, so I'm really confused by your statement. I use Unity since 2009 (version 2.6) and all your assets always have been inside the assets folder and it was the only one visible in the project view. Yes in the distant past when there were no packages, the view didn't even view the "assets" folder as a node in the tree view because it was literally the root of that view. Since the introduction of the package manager we now have packages which do not live in the assets folder as they are managed by Unity itself and are essentially read only. Though the structure / folder where all your assets are located has not changed in over 12 years.

Your claim of

"new standard" where all project files are found in the assets folder?

Also doesn't make much sense depending on what you mean by project files. Yes, all your assets (scripts, models, textures, prefabs, scenes, audio clips, whatever) live inside the assets folder, this was always the case. However Unity always had "project files" it needs for the actual project management. Specifically the Library folder (which is essentially the AssetDatabase) or the ProjectSettings folder. However you had never seen those folders in the project view since the content of those folders are completely managed by the Unity editor. The only folder you usually care about is the Assets folder.