The Pipeline Tool uses Eto.Forms for a cross-platform GUI that looks native on all platforms. It comes with some native dependencies, including the ones you've listed. If you update your repo correctly (including submodules) these issues should be resolved.
You can't update MG without solving the merge conflicts. I recommend you update more often if you make changes to classes that are often modified. Alternatively, if there is anything worth putting in the official repo, you can considering opening an issue or PR to discuss merging it so you have less maintenance.