Beginning with version 1.13.26, re-motion mixins supports the replacement of the entire default master configuration with your own. This works along the lines of setting the active configuration. Use the static method
MixinConfiguration.SetMasterConfiguration (myCustomMasterMixinConfiguration);
If you want all threads to use that myCustomMasterMixinConfiguration, make sure to replace it BEFORE any call to ObjectFactory.Create (). Otherwise, the corresponding thread will get the DEFAULT master configuration instead of YOUR master configuration.