SQL Server Change Tracking and Replication
My understanding of Change Tracking is that it is per database transaction. This means that all changes that are part of the same transaction get the same SYS_CHANGE_VERSION.

I also understood that the SYS_CHANGE_VERSION is set during the commit of the transaction, so numbers are a) always ascending and b) may be interleaved. You should always process the records in transaction completion order.

See Obtaining Changes by Using the Change Tracking Functions for confirmation that VERSION is ever increasing.