It does offer freedom. However with freedom comes at least the potential for inconsistency, and inconsistency in core patterns becomes expensive very quickly once teams and projects scale up.
It's been a year since I wrote this - the project continues at higher pace than ever, and we've onboarded a lot of new developers. Having a clear pattern for dependency has been super valuable, and in fact devs have been able to self-identify our 'right' way of doing things.
You're also right that it wasn't our only problem. I was always keen to point out that Koin as a library wasn't the root cause. However it was, for us, a significant enabler of a serious problem - loss of architectural control.