The datasheet does mention in a few places that the 1 kHz clock is seperate from any other clock. Take a look at section 5.7(Page 69) and section 5.9.7 (Page77) Table 5-10, the last field.
Here are the quotes:
From sectoin 5.7:
The 1-kHz internal clock source is completely independent of any bus clock source and is used only by the RTI module and, on some MCUs, the COP watchdog.
From section 5.9.7:
The clock source for the real-time interrupt is a self-clocked source which oscillates at about 1 kHz, is independent of other MCU clock sources.
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