The major source of confusion stems from the following:
There is a group of Cretaceous feathered, flightless birds such as the Ornithomimosauria, and Oviraptorosauria.
These are secondarily flightless birds. They are "secondary" because they developed from flying birds.
In the idea I am presenting, they fit in as follows:
Pterosaurs ---> Primitive flying birds (eg. Dromaeosauridae, Enantiornithes, Troodontidae etc)
---> Primitive flightless birds (Ornithomimosauria, Oviraptorosauria, ) ----> Modern Ratites (ostrich, emu etc)
However in the dino-to-bird idea they are misconceived as having evolved from dinosaurs and they are thought of as the forerunners to flying birds. So the dino-to-bird thinking has it exactly backward.
And the proof of this, is that flying birds were already around at the same time as the very earliest dinosaurs. (They may even pre-date the dinosaurs). The feathered, flightless birds (eg. Ornithomimosauria etc) developed from primitive flying birds.
The feathered, flightless creatures are not a transition from dinosaurs to flying birds.