Because Cura supports dual extrusion, it has to allow models to be positioned above the bed because there may be another model that will provide the support. It also allows models to be positioned below the bed surface and that portion below the bed will be ignored when sliced. I have used this to position an animal model whose feet were not “flat” on the surface. Moving it down a couple of layers worth until all four feet were “flat” on the bed.
Cura also has a preferences setting for “Automatically drop models to the build plate” which may not be set on your version. You can also right-click on a model and select “Arrange all models”. Cura also has a “Lay flat” option when you select a model and choose rotation.
An .stl model can be defined using any portion of the Cartesian coordinate space. Slicers will attempt to move them into the correct position in relation to the printer’s coordinate space, but they may need a little human help sometimes. The tools are there, you just have to use them.