Sort-of true on your second point. Flask gives you more room to organize the project how you want: if you don't have experience doing this then yeah, you'll make a mess. However, with experience comes more power. You aren't forced into doing things the "Flask way" because there is no "Flask way."

I think you're generalizing a little too much here. For something like an e-commerce shop, I'd agree. But for something truly custom, I find myself overriding a lot of Django's built-in functionality.

Kenneth Reitz made a presentation about this: https://speakerdeck.com/kennethreitz/flasky-goodness