Spirit System

I have changed my channel mapping around a few times, and based on the diagnostic tab they are all moving right now, however the channel number mapping in Spirit doesn't match what is in OpenTX. Is this OK?

Yes,

this is completely OK.
The reason for this is that by default mapping is different from Futaba. But S-BUS protocol is designed for Futaba including mapping. For this reason OpenTX need to change the mapping.