When a package has same name as base game one, the cooker uses the base game one

[Xymanek]

[0001.08] Error: Error, Ambiguous package name: Using 'E:\Programs\Steam\steamapps\common\XCOM 2 War of the Chosen SDK\XComGame\Content\XCOM_2\Maps\Cinematics\CIN_Skyranger\CIN_PostMission1.umap', not 'E:\Games\Mods\lwotc\LongWarOfTheChosen\ContentForCook\LW_Toolbox_Integrated\CIN_PostMission1.umap'

This means that while it's possible to override a package at runtime by providing one with the the same name, it's not possible to cook such a replacement package right now (the cooker will use the base game one)