Again, it is not strange.
The one checked in defines the defaults.
The one in the Gradle user home overwrites the defaults for the current user.
What is missing is another file in the project that is not checked in and has higher precedence.
Unfortunately Gradle guys are not really willing to do it, but you might also raise your voice in the according issue: Add official local.properties support · Issue #12283 · gradle/gradle · GitHub
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