Good news, API 1.7 for PowerPoint supports managing Custom XML Parts: https://learn.microsoft.com/en-us/javascript/api/powerpoint/powerpoint.customxmlpartcollection?view=powerpoint-js-1.7

await PowerPoint.run(async (context) => {
    const partsCollection = context.presentation.customXmlParts;
    partsCollection.load("items/id");
    await context.sync();
    //...
});