Hmm....when I've run mbrscan against Novell VM vmdk's, they've actually come back as aligned -- are you seeing otherwise?
Given that, I'd presumed that NSS was aligned by default....no alignment needed. See some mbrscan output below.... (3 disks per VM -- 1 for DOS, 1 for the SYS volume, 1 for the data volumes)
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/vmfs/volumes/7c1166f8-4da1ebe4/1Mail/1Mail-flat.vmdk p1 (FAT16) lba:32 offset:16384 aligned:Yes
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/vmfs/volumes/7c1166f8-4da1ebe4/1Mail/1Mail_1-flat.vmdk p1 (Novel) lba:32 offset:16384 aligned:Yes
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/vmfs/volumes/7c1166f8-4da1ebe4/1Mail/1Mail_2-flat.vmdk p1 (Novel) lba:32 offset:16384 aligned:Yes
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/vmfs/volumes/7c1166f8-4da1ebe4/2Mail/2Mail-flat.vmdk p1 (FAT16) lba:32 offset:16384 aligned:Yes
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/vmfs/volumes/7c1166f8-4da1ebe4/2Mail/2Mail_1-flat.vmdk p1 (Novel) lba:32 offset:16384 aligned:Yes
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/vmfs/volumes/7c1166f8-4da1ebe4/2Mail/2Mail_2-flat.vmdk p1 (Novel) lba:32 offset:16384 aligned:Yes