Not sure that's the problem since the makefile in question is auto-generated, unless I'm missing something.
I also just got my project to build by:
- Recloning my repo into a new directory on my PC.
- Setting the workspace as the directory in the repo that contains the Kinetis projects.
This "work around" seems odd to me since my original workspace (what's referenced in my original post) was outside of my repo location (one directory back), and I had never worked in Kinetis before on the project, so it's not like any project settings conflicted with each other. At this point, I don't know why what I did worked, but it did.
I always hate accepting the "start from scratch" method as a solution, so I'd love to hear other explanations/theories for future reference.