If you delete a program from the Programs folder, does it get uninstalled from the system? Nope. You have to go drag the registry and delete any mentions. You have to go looking for shortcuts and delete all those in multiple locations. If you go to the control panel -> add/remove programs, that works decently, but it's not guaranteed. It's been a couple decades since I've used windows regularly, but there were all kinds of folders, appdata roaming and that's just what I remember having to go dig through because there is no real standard for anything. That doesn't even get into system files and dlls.
There are package managers for Windows too. Choclatey is something I have seen in README.md files for various install instructions.
The Unix-like install locations are for organization. Goes back to Unix-like server oses. Linux is Unix-like as well. Linux doesn't have a registry to keep track of all the locations for all the files and configurations for each program, so organized locations where the system can expect to find specific things is how it's done. I much prefer the organized file structure, digging through the registry where there is only the minimal organization was something I always hated.
This is actually how things were prior to HMO's.