How do I fix my labels that dont have a mapping to avoid looking in MODULEPREFIX.ModelName.ModelLevel syntax?

This is determined by the RunMode value in the Instance Config xml:

From install-staging/build.properties, the possible values are "development" and "production", and they behave as follows:

# This property determines how labels should be displayed in the UI when
# a field for any category (normal as well as UDF) has no localized message.
# In 'development' mode the system will display the resourcebundle key e.g. meta.field.SysSiteId,
# while in 'production' mode the system will display the resourcebundle key in a more readable form e.g. Sys Site Id
# Values are 'production' and 'development', where 'production' is the default value.
# Developers can override it to 'development' in local.properties to easily detect the missing key value
server.run.mode=production

In my case, the RunMode is already set to production in instance_config, however I am still getting the key as is (i.e. SCC.trackingevent.sourcemodellevel.SCC.ProductionOrder).

Seems ResourceMessageBundle loads the localeToBundleMap with LaxResourceBundle which returns the key if no actual value is defined. This will bypass the translateValueToLabel feature Greg described above.