Why can I create a SharePoint list from the Site Content page and also create a an app of type "Custom List"? They both create a "Custom List".
What is the underlying difference?
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It is just two ways to create the same thing. There is no difference.
If you are wondering about the difference between a Custom List and other list types, a Custom List is just a bare-bones list that you can customize by adding columns. However, you can do that to any list so it's not really that different.