Reproduction steps:
1. Open the attached project "smallerProject.zip";
2. Build the project on Android platform;
3. Check "Minimum API Level" in Player Settings;
4. Check "Minimum API Level" in Assets/Plugins/Android/AndroidManifest.xml;
5. Check "Minimum API Level" in Temp/StagingArea/AndroidManifest.xml;

Actual result: In Player Settings "Minimum API Level" is set to 16. In both AndroidManifest.xml "Minimum API Level" is 10.
Expected result: In both AndroidManifest.xml "Minimum API Level" should be 16.

Note: The minimal selection in "Minimum API Level" is 16, so in Temp/StagingArea/AndroidManifest.xml "Minimum API Level" can not be set to 10.

Reproduced with: 5.6.0b3, 5.6.1p1, 2017.1.0b6

Can not be tested with older versions than 5.6.0b3 because there the minimal value in "Minimum API Level" is 9.

Verified with 2017.2.0b2