As long as you don't enable disk shares, you are ok with SMB.
When working with /mnt paths, as long as you stay totally within /mnt/user you are totally fine.
Don't mess with /mnt/diskX or /mnt/cache until you understand exactly why I'm telling you not to. When you understand what's happening behind the scenes, it's easy to avoid corrupting data, but until you have a good grasp, it's safer just to stick with /mnt/user.
As you've figured out correctly, user shares are simply the contents of /mnt/user. Keep in mind that windows can't handle folders with case differences, but the command line can. So writing files to /mnt/user/Photos and /mnt/user/photos is going to cause confusion in windows, but your scripts on Unraid won't care, it's two different folders to Unraid. Be careful to stay case consistent.
Docker containers add a wrinkle, the paths inside the container are mapped to paths on the host. So, if you have dupeguru mapped with
host - /mnt/user
container - /UNRAID
for example, you would find all your user share folders in the /UNRAID folder inside dupeguru.
All this and more is covered in the FAQ's pinned around the forum.