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When you add an invalid type to the choices of a value[x] element in a profile, validating the StructureDefinition succeeds without any errors. See for example the attached profile, where I've added a Reference type to the Questionnaire.item.option.value[x].
I am only now reading this thoroughly, this is not about an instance conforming to a structuredefinition, this is about the fact that when you create a structuredefinition, you can use datatypes in value[x] that are not in the base for that structuredefinition.
That's right, the validator does not catch that: there simply isn't any computable rule in the FHIR spec that specifies this behaviour (e.g. using FhirPath as an invariant). It would probably will have to be hand-coded into the validator.
When you add an invalid type to the choices of a value[x] element in a profile, validating the StructureDefinition succeeds without any errors. See for example the attached profile, where I've added a Reference type to the Questionnaire.item.option.value[x].
MyQuestionnaire.StructureDefinition.txt
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