This is what the creator of SuperDuper replied about cloning:

It's always "most reliable" to copy a totally inactive system from a 3rd drive. But it's sufficient, in most cases, to run from the drive you're copying from.
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--Dave Nanian

Alex
3.1 GHz 13" MacBook Pro 2015, 8 GB RAM, OS 10.11.2, Office 2011, TimeWarner Cable
2.8 GHz Xeon Mac Pro 2010, 16 GB RAM, OS 10.11.2, Office 2011, LAN