If an implementation guide has Extensions on NamingSystem, CodeSystem, ValueSet, ConceptMap or DataElement, that are defined in the IG, then errors will be generated that these extensions are not permitted.

(setting the profile in the resource will result in a warning that the structure definition can't be resolved)

Hint:
https://github.com/HL7/fhir-ig-publisher/blob/1ba4ad3ce5cbe06611a68bea057a60c0abde1152/org.hl7.fhir.publisher.core/src/main/java/org/hl7/fhir/igtools/publisher/Publisher.java#L2852
The structure definitions are cached into the context during the load(), not the scan() which results in the fetcher not being able to find them, and hence fails to validate correctly.
To fix this I moved the StructureDefinition to the top of the load() calls in the block, alternately the scan could cache the StructureDefinitions too.