It turns out that the game checks the amount of companions allowed into the party by checking whether both Player 1 and Player 2 have lone wolf. Because this mod doesn't give Lone Wolf to Player 2, the game allows 1 companion to be recruited into the party even though Player 1 has Lone Wolf. Two companions can't be recruited however.

Due to a request on the Steam Workshop thread for this mod, I am posting this modified bit of Story script in case someone else wants something to reference in the future:

This makes it so that any character upon level up will receive the additional points

Code
INIT SECTION
DB_AdditionalAbility(2,2);
DB_AdditionalAbility(3,2);
DB_AdditionalAbility(4,2);
DB_AdditionalAbility(5,2);
DB_AdditionalAbility(6,3);
DB_AdditionalAbility(7,3);
DB_AdditionalAbility(8,3);
DB_AdditionalAbility(9,3);
DB_AdditionalAbility(10,4);
DB_AdditionalAbility(11,4);
DB_AdditionalAbility(12,4);
DB_AdditionalAbility(13,4);
DB_AdditionalAbility(14,4);
DB_AdditionalAbility(15,4);
DB_AdditionalAbility(16,4);
DB_AdditionalAbility(17,4);
DB_AdditionalAbility(18,4);
DB_AdditionalAbility(19,4);
DB_AdditionalAbility(20,4);

DB_AdditionalAttribute(2,1);
DB_AdditionalAttribute(4,1);
DB_AdditionalAttribute(6,1);
DB_AdditionalAttribute(8,1);
DB_AdditionalAttribute(10,1);
DB_AdditionalAttribute(12,1);
DB_AdditionalAttribute(14,1);
DB_AdditionalAttribute(16,1);
DB_AdditionalAttribute(18,1);
DB_AdditionalAttribute(20,1);

DB_AdditionalTalent(3,1);
DB_AdditionalTalent(7,1);
DB_AdditionalTalent(11,1);
DB_AdditionalTalent(15,1);
DB_AdditionalTalent(19,1);


KB SECTION
PROC
ProcAdditionalAbilities((CHARACTER)_Player)
AND
CharacterGetLevel(_Player, _charLevel)
AND
DB_AdditionalAbility(_charLevel, _abilPoints)
THEN
CharacterAddAbilityPoint(_Player, _abilPoints);

PROC
ProcAdditionalAttributes((CHARACTER)_Player)
AND
CharacterGetLevel(_Player, _charLevel)
AND
DB_AdditionalAttribute(_charLevel,_attPoints)
THEN
CharacterAddAttributePoint(_Player, _attPoints);

PROC
ProcAdditionalTalents((CHARACTER)_Player)
AND
CharacterGetLevel(_Player, _charLevel)
AND
DB_AdditionalTalent(_charLevel, _talPoints)
THEN
CharacterAddTalentPoint(_Player, _talPoints);


IF
CharacterLeveledUp(_Player)
THEN
ProcAdditionalAbilities(_Player);
ProcAdditionalAttributes(_Player);
ProcAdditionalTalents(_Player);