ATMega328: How to select alternate function on a pin
Specific to timer/counter control register A, register TCCR2A bits 7:6 COM2A1:0 control whether or not the internal OC2A signal overrides the normal PORTB3 pin behavior. See datasheet section 17.11.1 TCCR2A – Timer/Counter Control Register A - found by searching within the datasheet for OC2A.

The section you referenced 13.3 Alternate Port Functions gives a generic description of how all of the alternate port functions are worked out, but only goes as far as the override signal names. See table 13-5 for Overriding Signals for Alternate Functions in PB3..PB0. They give a bunch of Boolean expressions for each of the overrides -- PVOE is "Port Value Override Enable" and PVOV is "Port Value Override Value" as per the earlier diagram 13-5 Alternate Port Functions. To find out which actual bitfield in which register controls each alternate pin function, you have to search the signal name within the datasheet.