Right now, using Calibre's Convert to change epub3 to epub2 (look for Epub Version on the 'EPUB output' section of Convert settings) before using EpubMerge is all I can offer you.
I have yet to see any particular advantage to epub3 over epub2, myself.
If I were to make any changes to EpubMerge / EpubSplit for epub3, it would be to automatically call Convert epub3->epub2.
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