Is there any way to add objects to InstanceObject in rhinocommon? I am familiar with modifying Instance definition using doc.InstanceDefinitions.ModifyGeometry(). But I want to add a certain geometry to an instance object and not to the definition (just like we double click a block reference in rhino and add an object, and every block reference including the definition gets updated). Thanks.
Sorry no. Instance objects on reference their underlying instance definition.
You might consider exploding the instance object, adding your additional geometry, and then making a new instance definition.