An application that consumes or produces Open XML should never care what the name is of the workbook part. Identification of parts is never done via the URI; instead it is always based on content types and relationship types. It is a bug in these other libraries / applications if they stop working based on the actual URI of any part.
I understand that this doesn’t help us – we need to use libraries and applications that may contain bugs. However, I do not anticipate that such a change will be coming to the Open-Xml-Sdk.
Have you raised this issue with the maintainers of those other projects?
Alternatively, you could use System.IO.Compression to go into the XLSM and change the name of the workbook part. It would not be hard. However, you would need to be careful to do it correctly.
Are you fully familiar with the Open Packaging Conventions? If not, watch screen-casts 11 and 12 in the following series:
Introduction to Open XML
Cheers, Eric