Adjusting defaultSpeedMap in custom CarFlagEncoder has no effect

For a specific road type, say secondary, I can adjust the vehicle speed

Yes, in the new format (either JSON or YAML) this would be:

speed:
 - if: road_class == SECONDARY
   limit_to: 80 # without this value it picks the default from the Java code

In master branch there is an editor with auto completion to help you create these scripts.