A publication cannot point an object already published more
than once. When creating the import link, the published object is looked for
and the import is created on the first publication found which might not be
the one that has the same name as the input.
The only information that the Document Template can provide is the final object itself (infrastructure prevents you from specifying the publication, enabling you to select only the pointed object). The publication is then automatically retrieved by the link infrastructure.
Workaround: Create meaningless geometry that uses these inputs in the same part.