The issue was caused by Render Single Layer option enabled, which is very handy for artists work, so they can hit F12 and see view layer they are currently working in a final rendered state. This saves a lot of time since all the "non-interesting" objects are ignored for such iterations. However, for the render farm we need to render view layers which are explicitly set for render, and ignore active view layer. Reasonable solution seems to be to ignore the Render Single Layer option when rendering from the command line. It is really something more like UI behavior option.