The waveforms of fig 41 make perfect sense. Exactly the way I imagine things.
But... page 54 of that same manual says:
"When the timer counter reaches the modulo value, the TOF flag is automatically set by hardware, and the timer counter resumes counting from $0000 at the next clock."
That appears to say the TOF is set 1 count before overflow...
Although, if we set the modulo to say 50 then it counts up to 49 and then rolls over to 0 for a 50 count cycle. If we say zero is the final (i.e. modulo) count then the statement in the manual makes sense - I think.