Your question can be interpreted in two different ways:
1. Is it allowed to have two classifications for the same Submission Set -- one inside, one outside?
2. Is it allowed to have in the same message (e.g. in an ITI-18 response) a Submission Set with an inside classification and a Submission Set with an outside classification? (E.g. if different Document Sources use different approaches, and the Document Registry does not re-structure their submissions.)
From my point of view, the both questions can be answered with "yes", as there are no inconsistencies in the XDS metadata.
Independeptly from all that, there may be a schizophrenic situation where the same RegistryPackage is classified both as a Submission Set and as a Folder. And this will even pass the validation it the said RegistryPackage contains all attributes necessary for the both object types.
Best regards
Dmytro