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Like ObjectTables, EncounterTables.xml supports MergeLoad="trueMerge" in the object root tag. This will append entries to that particular table instead of overwriting.

PopulationTables currently do not have limited support for modding, but many zone template encounters draw objects from dynamically created population tables. Check out the following tags in ObjectBlueprints.xml to see them in use: DynamicObjectsTable, ExcludeFromDynamicEncounters. Some dynamic population tables are created based on the base type of the object, so new objects will begin appearing immediately in areas generated with dynamic population tables unless they are tagged with ExcludeFromDynamicEncounters.

The unaffiliated cave systems are the only areas currently heavily populated with the template+population system.

Extending Encounter Tables

You may add new entries to existing encounter tables by including EncounterTables.xml in your mod, using an existing table name and setting the Load="Merge" property on the encountertable tag.

<?xml version="1.0" encoding="utf-8"?>
<encountertables>
  <encountertable Name="Ammo 1" Load="Merge">
    <objects>
      <object Chance="100" Number="3d6" Blueprint="My New Ammo"></object>
    </objects>
  </encountertable>
</encountertables>

Adding and Replacing Population Tables

You may add new population tables and replace existing ones by including PopulationTables.xml in your mod.

<?xml version="1.0" encoding="utf-8"?>
<populations>
  <population Name="MyMods_SmallGunAssortment">
    <group Style="pickeach">
      <object Blueprint="Borderlands Revolver" Number="1-3"></object>
      <object Blueprint="Semi-Automatic Pistol" Number="0-2"></object>
      <object Blueprint="Chain Pistol" Number="0-1"></object>
    </group>
  </population>
</populations>

Additional Info

Here's a thread on Steam where I discuss using encounter and population tables: http://steamcommunity.com/app/333640/discussions/3/358415738194955181/