Q: If both "handling time in settings" and "Override default handling time" have a number, which one do you follow, the handling time in the settings, or the "Override default handling time"?

A: You should always have a handling time in your marketplace settings, otherwise the number 5 is assumed.

If the individual item has an override default handling time, then the override default handling time is assumed and the handling time in the default settings is ignored.  Anything that is an override in Sku Grid takes precedence over general settings and causes Sku Grid to ignore the default settings.