So I thought that I did a simple merge from my feature branch back down into master. However, in Git Extensions it's showing labels a couple of revisions back in a faded style (see image). What the heck is this supposed to mean? The documentation is extremely lacking. If I do a git status on both the master and the branch it says that there's nothing to commit and the working tree is clean.

What you're seeing is the effect of these two settings in Git Extensions:
Basically, the repository you've shown the history of is a submodule of a surrounding repository. The submodule repository have two commits that the parent repository isn't aware of yet.
Let me explain.
When you commit in a repository which has a submodule, the sha of the commit the submodule repository is at is recorded in the parent repository. Thus, the parent repository thinks the submodule should be at that third commit.
However, the repository in that submodule has a life of its own, and after the parent repository was told to use that third commit, another two commits has been added to this submodule repository.
Those washed out labels signifies where the parent repository thinks the submodule should be.
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