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From what I've seen the ros2 launch <pkg> <launch_file> method is the "proper" way of doing it. If I had to guess I would say that the example you linked is structured as-such so as to make it self-contained in some way.
As for problems... You might run into weird issues if/when you start trying to reference launch descriptions within each other. E.g. you have a launch file for Node A, one for Node B, and another for Node C. Then you have a "master" launch file that imports some combination of each, and perhaps adds a few other things on top like log levels or miscellaneous ROS command line arguments. I can't say you'll 100% run into problems with the latter approach of using python3, but with the former approach with ros2 launch you'll definitely have no weird behaviors crop-up.
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