Some anecdote you might find helpful concerning the current state as you are specifically asking about atom on windows 10.
Some of my students (atom on windows 10) encountered a situation where they could not get the plot to display consistently, often it would not update or most of the time not display at all. Might be an istance of this one or something else, I did not investigate in depth.
My personal workflow for years has been to use whatever plotting package works (usually gnuplot on linux :-), export a vector format (.svg or in olden times .fig) and then to move legends, labels and change fonts/ font sizes as I like later.
This is a very good suggestion if it is not possible to script/ automatize the plot generation completely and the vector format is small enough in size. Might be complete FEM meshes are a bit much for that, though.