I think I have found the solution to this problem: cherry-pick --strategy=recursive -Xtheirs <commit-SHA>
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Specifying the 'theirs' option in recursive merge strategy forces conflicts to auto-resolve cleanly favoring the version that's being merged in. This will ignore all the conflict warning but grab whatever is in the commit.
I guess now I just want to know why cherry-pick would produce a conflict warning when picking a commit that modified an existing file in the current branch, even if just adding a line.