Richard Joye comments

Of course I can imagine it being nice,.... Shibuya crossing with 1/10th of the people, great discounts, restaurants usually fully booked now offering tables and even discounts.

But the problem is the traveling part... coming back from Japan, many countries now impose restrictions.

One thing: the event is NOT canceled. 

"The Tokyo Marathon 2020 will be held only for the marathon elites and the wheelchair elites."

So in such case, Entry Regulations Article 13. should not apply. This applies only in case of event cancelation. 

Tokyo Marathon will still be held. They decided to restrict it and remove other categories. Same as when they decided to remove a citizenship/place of origin/residence as China. They offered refund in this case and free entry fee next year. 

They did not 'cancel' then even for Chinese.

They don't cancel the event for general entry. They restrict the event to 2 categories. 

Then ? 

They should reimburse or offer free entry next year.