The developers' change log indicates that more name lists *might* be in the next patch, when/if it is released.
For now however, yes, that is the only way to explicitly name a unit and there are only 2 slots.
Some workarounds people have used:
- Specify the unit name in the description, and just assume the player will rename the unit. This is safe, if unsatisfying.
- Use the name list for a nation that is not in the same era as a particular mod (e.g. Bogarus' name list for an EA/MA mod.) This has been used often enough that it's about as susceptible as the custom name lists to being overwritten.
- Come up with hero concepts that don't rely on a specific name, e.g. give the unit type name "Masked Avenger" and you don't really care that the unit is named "Bob".