Finally after we've clarified the problem.
The project_template component should only be used for projects created by the new project wizard in the MCUX IDE. It is ignored in other use cases. That works as expected.
There was a problem with an incorrect dependency that was included by the meta-requires element in YML and was overriding correct dependency defined by the __requires__ element. Description of the meta-requires element from the Yml data record guide:
meta-requires: # optional, "meta-requires" tag is for the "requires" in manifest/cmsis pack. If "meta-requires" and "__requires__" exist at the same time, generator will use "meta-requires" for the "requires" in the manifest/cmsis pack.