Well no its simply not like that. Its a feature that the ambiance is utilized.
And I dont understand your problem. If you want to behave Eevee different for now and forever, then just enter the setup you asked for a single time and write it back to the start up file. Then blender does what you want.
This change gives you the option to set them independently and just for Eevee just as you asked for.
And this is how it will look for you from now on:
And if you want the background to influence the scene just change the upper color value to be the same as the lower one
Edit: Sorry I connected them together quickly. Just had a short look and its better to set it up like its now, I updated the screens. Still you can simply replace the default scenes setup with this.