Some ontologies need to have different namespaces for their URIs.
That can be specified with a header value in the OBO file but the OWL API needs
suppor that header instruction.
This does not sound like a bug but more like a feature request. It is a bit vague, you'll need to flesh out what kind of headers you're thinking of. An example would be great.
No, it is indeed a buglet :)
The parser should take idspace tags into consideration and it doesn't. Will fix.