This sounds more like an issue with the application design rather than Flask, Python, or even Web development. How easy or hard it is to test software is often

This sounds more like an issue with the application design rather than Flask, Python, or even Web development. How easy or hard it is to test software is often a good indicator of the quality of the underlying design - if it is too hard to separate code into testable units and you have to mock loads of things to test for the most basic cases, there's a more fundamental problem somewhere. Of course, there are things that are hard to test, but it shouldn't be the whole application that is hard to test.