Toronto is a mandatory MS1000 tournament, then if you are allowed to enter and don't take part, you get zero point for that event and can't replace it with another result.
The rule which allows Fed to skip 2 mandatory MS1000 tournaments this year is only for money/official excuses concerns, has no importance for teh rankings.
So, he will be able to count Doha after his Tokyo 0 pointer drops? Or does he have to play a 4th ATP500? Is Olympics treated as an ATP500?