There are tradeoffs of course: you give up the Django admin and a bunch of other things, at which point we might as well have used Flask. But our shop has a number of other "normal" pure-Django apps so it makes sense for us to use Django as a common base.
Awhile ago there was a book called "Lightweight Django" in which the authors showed how to use Django in a stripped-down Flask-like manner. Ultimately Django is just a big bag of parts that you can use or not use.
It's exactly the same situation: either you luck out, and someone already wrote all the conveniences and utilities and integrations with components for you exactly the way you want them with exactly the set of other components you wanted, or you do it yourself.
Also, you could make a similar argument about swapping major components into, say, Pyramid. Most of the alternatives people promote to Django are not really some paradise of trivially-swapped-but-tightly-integrated components. They just do exactly what Django does, with a different set of "use these or lose the integration" components chosen up-front for you.
But yes, with Flask (or similar frameworks/libraries), you need to do the integrations yourself with the components you want to use. Advantage of Flask in this regard is, you don't need to fight with Flask to make it happen. That's why I'm saying it's better suited for complex apps that you want to build with your own abstractions.
The real problem is the cargo cult thinking when it comes to frameworks, instead of doing a cost/benefit analysis and thinking about trade-offs.
Following statements like "Django for complex apps, Flask for 100 lines of apps" without researching the reasons behind probably will result in more problems in the future.
Really? So you got all the things you get in Django -- ORM, forms with validation, etc. etc. -- from "a few lines of code"?
Somehow I think that's not true.
I'm using Flask, but building my apps with Python.
This simple/complex equation should be reversed IMHO. Want to throw together something quick? Go with Django, where everything you need is built-in. Want to build a big app? Go with Flask, and build your stack specific to your needs.
As a bonus, once you have built a complex app with your own abstractions/magic succesfully, it becomes faster for you to build new projects with your own framework than any other alternative.