Under Ubuntu (Linux), when you use Anaconda, you are just changing the search path for programs. For example, type: env | grep ^PATH and note what it says.
Now, if you have created an environment called foo and then activated it by typing conda activate foo, then you will now see the (foo) prompt.
After you do that, type env | grep ^PATH again. And you will see that the location of the "foo" environment has been placed earlier in your PATH. Programs are sought a directory at a time, starting from the front of the PATH.
If you're in the "foo" environment, your terminal will search for programs in "foo", then the base environment (i.e., the environment which is the parent to all other environments), and then the system.
By default, when you log in, the "base" environment activates. That is what you're seeing. If you want to disable it, create a file called ~/.condarc (or edit it if there's a file there already) and add this to it:
auto_activate_base: false
Log out and log back in and the "base" environment will no longer activate automatically. If you have a program called "bar" installed within the system, within the "base" environment, and the "foo" environment, it's possible that they could be 3 different versions. It's always useful to use the which command to see where the program you are running is located in. i.e., type which bar.
And yes, you can run "normal non-Anaconda" commands. It will search for programs based on your PATH setting. If you have activated the "foo" environment and you want to run a program explicitly in the system, then you can also just provide the exact location. i.e., /bin/bar. Anaconda doesn't "hide" the system from you -- it just changes the priority when looking for programs.
(I can't answer your question about comparing against Windows because I have never used it with Anaconda.)
Hope this helps!
