Query object are created by Propel during the build model step. See the schema definition for details how to describe them in XML.
As you can see src/Orm/Zed/ the query object which belongs to the Spryker core extend base classes placed in the vendor directory. This way you can easily adopt the classes for your needs but we can still add methods in the core.
Query class generator
The Propel module alters the rules of generating query models by requiring explicit passing of filtering criteria into filterBy.. and findBy... methods.
This means, that when an array, LIKE expression or an array with min/max are passed as a filtering argument, it is explicitly required to specify Criteria::IN, Criteria::LIKE or Criteria::BETWEEN.
The Criteria::BETWEEN is implemented in the wrapper class Spryker\Zed\Propel\Business\Runtime\ActiveQuery\Criteria.
Additionally the Propel module adds the following methods into the generated classes, that allow to easily filter: filterBy...._In(), filterBy...._Like() and filterBy...._Between().