Assuming that "Windows Server Containers" are based on the Drawbridge technology that's been around Microsoft for a few years, the containers can only mess with other containers to the extent that you've configured them to be able to.

I used Drawbridge to implement R support in the Azure Machine Learning service two years ago (as referenced at https://redmondmag.com/blogs/the-schwartz-report/2014/10/win... ), but I haven't worked on it since so I don't know how things have evolved.