Currently, when we define the custom hierarchy, the parent-child relation can be configured between consecutive issue-type levels.

Hierarchy level :

• Sub-task (Level -1)
• Story ( Level0)
• Epic/Feature ( Level1 )
• Program Level2 )
• Initiative ( Level3 )

Parent-child relationship (Present scenario)

• Sub-task -> Story (Jira internal child/parent association through 'parent' )
• Story -> Feature ( through 'Parent' due to consecutive level association)  
• Story -> Epic (through 'Parent')
• Epic/Feature -> Program (through 'Parent' due to consecutive level association)
• Program -> Initiative (through 'Parent' due to consecutive level association)

We don't have the ability to link Initiative directly with Epic/Feature. Users should be able to bypass/skip any custom hierarchies and link the issues to something like the one below.

Parent-child relationship :

Story -> Program ( parent ) 
Story -> Initiative  ( parent )
or Feature -> Initiative ( parent )