Possibly I miss something but I'd expect the internal item zabbix[process,configuration syncer,avg,busy] to reflect the busy time of the configuration syncer process as seen in the process table.
The CacheUpdateFrequency is not configured thus should be set to the default value of 60 seconds.
A look at the process title confirms that assumption. Between configuration synchronizations the configuration syncer process is idle for one minute. A synchronization takes by the way never more then 10 seconds.

Now why looks the historical data of the internal item so differently?

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