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Yes, I typically use Sigil's epub3 tools to remove both the guide and the ncx as epub3's do *NOT* use them.
If, after all editing is done, I decide I want an epub3 that is backwards compatible with an old epub2 only e-reader, then I use the Sigil's epub3 tools to create them as they will then be properly synced with the final Nav.
Luckily the days of older epub2 only e-readers are fast coming to a close.
FWIW, I also run the Sigil epub3 tool to check and update all the OPF manifest properties once just before the final save especially if I add remote resources, javascript, or mathml.
Those are all tools that need to be run by the user only once just before running a final epubcheck and final save.
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