How to choose which related contact gets the membership by relationship
The only way i know that you could do this would be to use a different relationship type

So base the inherited membership off eg "is child org member of"

So a child org that is not a member could have relationship of 'is child org of'

while the 3 that you are talking about could instead/also have 'is child org member of' relationship

if you were happy doing a customisation then you could change the inherited relationship feature and set it to only trigger if a custom field on the relationship is set to 'yes' for example