I don't see #1 happening. There is no way anyone has my personally customized development setup in some VM ready to use. More likely it is going to be one common setup that they want everyone to use.
Why would your personally customized development setup even need to be on the remote host? You pop up your IDE, connect to the remote host via SSH and you are set.
It's great too because if your own environment breaks, you can compare to a working one to fix it.
Just because a company might abuse it doesn't mean we should avoid it.
IE. it's no slam dunk. Like any other tool of this sort is will be used for good and ill.