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I think you have to stick with the CustomSectionXMLGenerator, but since it doesn't handle colons (:) properly you have two options:
1) Log an enhancement/bug request.
2) If you can't wait for that to be fixed, you theoretically could temporarily modify the value of the custom section name in memory prior to passing it to the GenerateXML method.
-> instanceDO.SectionTemplate.NameML.Name -- replace the colon with an underscore or something similar. If you wind up using the instanceDO again after, you could restore the value, but if you don't use it, then it doesn't need to be restored (assuming you aren't saving the DO or its parent object.
If you need to update the rows too, you could do so by looping through the rows
foreach (IExtendedAttributeRowInstanceDO rowInstanceDO in instanceDO.Rows.OrderedValues)
Thanks Ron, the workaround should be fine in our case. We'll put in a SR/request as well.