The TCNT counter value is used to calculate microseconds outside the interrupt. Using a comparison match to determine the TOP value will lead to an exact interrupt, but complicates the calculation of thinner micros, since TCNT reset. Using comparison comparisons for non-TOP values (for generating PWMs) does not generate a 1 ms periodic interrupt.
I personally use as the second timer to select the TOP value defined by the OCRxA register.
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