Creating a filter layer.

    # first, create a filter.
    desaturateFilter = Application.filter("desaturate")
    # get the config, and modify it. You can get the parameters from the 'xml' button in the filterdialog.
    config = desaturateFilter.configuration()
    config.setProperty("type", 2)
    desaturateFilter.setConfiguration(config)
    #Setup a selection, you need this for the filter layer.
    selection = Selection()
    selection.selectAll(exportNode, 255)
    # input everything into the filterLayer function.
    filterLayer = exportDoc.createFilterLayer("desaturateLayerName", desaturateFilter, selection)
    # add layer to document
    exportDoc.rootNode().addChildNode(filterLayer, exportNode)

Thank you Wolthera! I made a few customizations to tailor it to specific needs:

• Only copy paintLayers because I didn't know how to programatically create the right filter you show me just above. So I decided to create a filterLayer at the top of my Storyboard file and copy it once each loop but not as a single file.
• No save dialog but directly saving in ../kra)
• Resize the exported image to fixed width
• Changed the call to setChildNodes to addChildNode (the setChildNodes call would erase the Background layer which I need)
• index with 1 padded 0
• set the active layer in the new file (line 42). But it doesn't work for now. Any idea ?
• Now this might be dirty but I used a lot of global variables to be able to set them all in one place and customize the script easily

Here my take on it export_layers_to_seperate_kra_files.py

Here is my way to add a solid white background on an existing file.

from krita import *
import glob, os
chapterPath = "Path to your base folder"
os.chdir(chapterPath + "Path to your png folder")
for f in glob.glob("*png"):
    # retrieve the document and create a view
    doc = Application.openDocument(os.path.realpath(f))
    window = Application.activeWindow()
    view = window.addView(doc)
    window.showView(view)

    # create a paint layer and put it at the bottom
    paintLayer = doc.createNode("Background", "paintLayer")
    root = doc.rootNode()
    children = root.childNodes()
    root.setChildNodes([paintLayer, children[0]])
    # fill the layer with white
    data = ([255] * doc.width() * doc.height())
    paintLayer.setPixelData(bytearray(data), 0, 0, doc.width(), doc.height())

    # Add a desaturation filter
    # first, create a filter.
    desaturateFilter = Application.filter("desaturate")
    # get the config, and modify it. You can get the parameters from the 'xml' button in the filterdialog.
    config = desaturateFilter.configuration()
    config.setProperty("type", 2)
    desaturateFilter.setConfiguration(config)
    #Setup a selection, you need this for the filter layer.
    selection = Selection()
    selection.selectAll(children[0], 255)
    # input everything into the filterLayer function.
    filterLayer = doc.createFilterLayer("desaturateLayerName", desaturateFilter, selection)
    filterLayer.setVisible(False)
    # add layer to document
    doc.rootNode().addChildNode(filterLayer)

    # save and close the document
    doc.saveAs("Path to your kra destination")
    doc.waitForDone()
    doc.close()

At first I tried to make a FillLayer but I realized it's not a paint layer. Then I tried to merge a paintLayer down on the fillLayer but it happens mergeDown makes krita crash. See issue 419093 Not only that but a newly created FillLayer will appear transparent until I toggle it's visibility by hand (refreshProjection and scripted setVisible won't work)