Tested regular freestyle job with Maven build step (top level)
Simple Java EE 7 war file
Selected Settings File (MySettings)
Executed job.
No errors but MySettings was not used and there was a warning in the console log from MvnSettingsProvider.java (line 80)

listener.getLogger().println("ERROR: your Apache Maven build is setup to use a config with id " + settingsConfigId + " but can not find the config");

Downgraded to 2.13
Ran the test job
Success:
using settings config with name MySettings
Replacing all maven server entries not found in credentials list is true