I've had many courses that were bogged down by software setup issues in college; I would rather than not be the case.
I want to say that, if it's pedagogically valuable, then it needs to be made into a small lab course (or part of the lab unit for an intro class), and taught once, in an organized manner.
And then stop letting professors hide behind this lame excuse so that they can get on with teaching the stuff that their course is actually about.
(I am actually leading a machine learning for high-schoolers camp in 2 weeks and we are using Jupyter notebooks so that all students, with heterogeneous backgrounds, will start in the same place and get to the fun stuff fast. Many will never have used Python and will not know or care about 2.7 vs 3, just to give the most high-level and basic example!)
An exception would be the example of the deep learning project work. In this case JupyterHub was utilized as an easy way to deploy a centrally managed, cost effective environment for a large class to use GPU resources without the risk of running up huge AWS costs for each student.