GenericPositionPair XML:
<mapped-superclass name="GenericPositionPair">
<indexes>
<index columns="position" />
</indexes>
<field name="position" type="integer" column="position" />
</mapped-superclass>

GenericPrimaryPositionPair XML:
<mapped-superclass name="GenericPrimaryPositionPair">
<indexes>
<index columns="isPrimary" />
</indexes>
<field name="isPrimary" type="boolean" column="isPrimary" />
</mapped-superclass>

PrimaryPositionPair XML:
<entity name="PrimaryPositionPair" table="PrimaryPositionPair">
<id name="first" type="integer" column="first_id" association-key="true" />
<id name="second" type="integer" column="second_id" association-key="true" />
<many-to-one field="first" target-entity="First">
<join-column name="first_id" referenced-column-name="id" />
</many-to-one>
<many-to-one field="second" target-entity="Second">
<join-column name="second_id" referenced-column-name="id" />
</many-to-one>
</entity>

PHP:
PrimaryPositionPair exteds GenericPrimaryPositionPair
GenericPrimaryPositionPair extends GenericPositionPair

Finally - the resulting SQL statement contains no idexes on position and isPrimary fields.

Suggestion - wouldn't it be easier to just include attribute index="true" instead od <indexes> tag, since attribute unique="true" already works.