From the remarks of IBomFeature::Configuration:
You cannot use this property for top-level only BOM tables because information on multiple configurations can be shown at once in that style table. In that scenario, getting this property returns an empty string and setting the property has no effect. Use the IBomFeature::GetConfigurationCount, IBomFeature::GetConfigurations, or IBomFeature::SetConfigurations for that type of table.
IBomFeature::GetConfigurations solves the problem.