Yes, the description is little bit confusing, what is main timer and what is counter.
There is 16-bit Free Running Main Timer derived from the bus clock via prescaler. So we can say it is a clock.
The timer counter (TCNT) is the part of the module and that is 16-bit register which counts up from 0x0000 to 0xFFFF.
Maybe i'm not exactly correct about this, but at least it's not that confusing.
If enabled, Timer Overflow Interrupt (TOI) is triggered each time Timer Overflow Flag (TOF) is set.
Timer Overflow Flag (TOF) is set when the 16-bit timer counter overflows from value FFFF to 0000.
Timer overflow counter can be used to measure periods longer than one timer period.
Attached are some old project demonstrating the frequency measurement on S12XDP512 device.
The CodeWarrior projects are compatible with the latest v5.1 version.
Hope that helps.
Regards,
iggi