The the current new_units.py and the shell commands listed in the HOWTO do not preserve the command index of the ability when populating ability_lookup.csv. This means that the abilities with the same ability link but different command indices end up mapping to the same ability id.
This can be easily verified by loading a replay (with game events) where the player builds a supply depot and a barracks. The supply depot command event will have the correct ability name, but the barracks command event will not.