What is so special about them?
To answer your question directly, for some reason the first three sections are parsed as wikitext, while the remaining ones are not.
$out->addWikiText( $this->getMediaWikiCredits() . $this->softwareInformation() . $this->getEntryPointInfo() ); $out->addHtml( $this->getSkinCredits() . $this->getExtensionCredits() . $this->getExternalLibraries() . $this->getParserTags() . $this->getParserFunctionHooks() );
Why it is so, no idea. It would be good to make this consistent, in one direction or another.
I would actually prefer to generate HTML output in the first three sections too, as that's how most special pages are done. They already are mostly HTML-based, the tables and text formatting are done with plain HTML that the wikitext parser just passes through; it would primarily be the matter of changing link generation.