Glad you love the new version.
As you have found, R+J is not handled consistently through the ecosystem. Most apps (like Photos) edit the JPEG. RAW Power chooses to edit the RAW. There isn’t a way to edit the JPEG version right now. I plan to add a control to let people decide (this has always been true, but many people have suddenly started asking this same question). It’s technically possible to split the R+J apart, but it’s complicated to do it correctly because the only real way to do it is to import a new RAW and new JPEG asset and then delete the old one.
Batch Processing follows the same rule – it edits the RAW only. That’s one of the complications of offering an R+J switch. Batch Processing would either need to prompt or use a preference. However, I don’t know if either is a good solution.