Might be a little late, but Lakelurks are members of both the LakelurkFaction and the CreatureFaction, if the mod only makes MirelurkFaction and LakelurkFaction allies but not MirelurkFaction and CreatureFaction, Mirelurks and Lakelurks will still fight each other since Mirelurks are only members of the MirelurkFaction but not members of the CreatureFaction. I had the same problem with one of my mods.
tldr: Mirelurk Ally Lakelurk but not Creature = fight Mirelurk Ally Creature but not Lakelurk = fight Mirelurk Ally Lakelurk AND Creature = peace
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I had the same problem with one of my mods.
tldr:
Mirelurk Ally Lakelurk but not Creature = fight
Mirelurk Ally Creature but not Lakelurk = fight
Mirelurk Ally Lakelurk AND Creature = peace