As the owner of a general-aviation simulator based training center,
I believe that negative transference is a little more subtle and insidious
than is portrayed in this article. Certainly, there are obvious forms of negative transference as you point out.
However, there are more sinister types that need to be addressed for GA pilots
to avoid the risk of negative transference. Calling a simulator a "box" is
just one example. At our center, we refer to the device during training as
the airplane. The expectation is set from the start - the pilot or crew is
to operate it as if they were flying an actual airplane. Any other euphemism
is an open invitation to deviate from SOPs used in the airplane. How many times
I have heard "I would never do that in an airplane."
Speaking of SOPs, that is another serious source of negative transference.
There is a tendency for pilots training in a device to lose discipline, for
there is no real threat to loss of life or equipment as there is an airplane.
Again, we don't fly simulators - we fly airplanes.
There are many other culprits, one being ATC phraseology. This is typically an
instructor oversight, but failure to consistently use proper phraseology can be
a significant source of negative transference in the airplane - especially to
a new instrument pilot.
As the old adage goes, Train the way you Fly, Fly the Way you Train.
I don't think any of the things you mention are examples of negative transference, and none of them are a result of the sim not being up to snuff in any way. They are examples of poor training practices having a bad effect on the students--we've all seen these things happen. Your comments about using proper phraseology is right on the money. You're smart to nip bad practices in the bud and insist on doing things right. Kudos.