yeah, Rhino_DotNet from v5 has ModifyInstanceDefinitionGeometry which takes IRhinoObject[] but that (all instance-related apis, apparently) appears to have been removed in v6 Rhino_DotNet
and this seems like more than I would be comfortable doing (and apparently is not workable anyway, unless there is some rhinocommon way to create a definition with other than GeometryBase) inside ReadDocument:
I think custom objects should have read/write methods to override, and just work, without sketchy replacement going on in ReadDocument