YGE recommends that their internal governor should be used and Spirit recommends that theirs be used. Who is correct?

Both are right use the one that suits you better.
I use the governor from the Spirit unit, if you have integration (e.g. Jeti) it's easier to debug.

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Spirit System (Spirit W1, RS & GTR & all the others)
Spirit Wave & JETI DS 12
http://www.habada.cz

Even if you ultimately end up using the Spirit governor, you may want to consider letting the YGE governor determine the head speeds RPM the system can reasonably govern with the motor kv and gear ratio you are using. The head speed calculators get you in the ball park, but the YGE governor can tell you exactly what YOUR individual system can govern. Let the YGE ESC governor figure out what head speeds it yields at 80% and 85% throttle, and use that as the top head speed to enter into the Spirit governor software.