This is by design.
The coalescedSourceConfig contains what is gathered from that inis base, default and platform ini files.
Options from the coalesced config will be used at runtime unless the user has changes in the Saved/*.ini which then ultimately overrides this.
Note, The coalescedsourceconfig is generated on each run.
The settings .ini files for games packaged for windows appear to be getting overwritten with blank files whenever the game is run. Even if settings are added to the .ini files manually, the files become blank again the next time the game is run.
This appears to have been functioning as expected in version 4.4.3 (CL 2298372). The current behavior appeared in 4.5.0 (CL 2326468).
The GameUserSettings.ini file is blank again.
The GameUserSettings.ini file retains the settings.
Head over to the existing Questions & Answers thread and let us know what's up.