I don't know of any limitations or differences between APEWorker and SISWorker regarding bcf handling.
However, APE and SIS call a different application on PE. The SIS application may not be handling this rule in the same way. The difference may also be on the Windchill side and how it ingests SIS representations.
Since your bcf is working in APEWorker, than I would look to the differences between the 2 pipelines. I'd be interested to hear what PTC says about this.
I confirm that bursting is not applied when performing a SIS publising, because payload contents are built on Windchill side, and are not retrieved by APE like for a PE publishing.
I you want "up to date" WC metadata property values to be applied for your publication, you should configure publication to embed them in the manifest. Then a compositionframeworkhook on APE side may read this information from the manifest and use it.