Past perfect is used to suggest that something is over and done with before the main action of the past. It would be OK to say:
The 1972 agreement replaced the amount of phosphates that had been allowed with a new amount.
But if you are talking about changing an amount, then the amount existed before and continues to exist after the 1972 agreement. The present tense is used to refer to something that exists for all time.
Copernicus revealed that the Earth and the planets all revolve around the Sun.
"Revolve" is in the present tense because it is an action that was then and continues to take place. It would be wrong to say: "...revealed that the Earth and the planets revolved..." or "had revolved."
In the sentence under dicussion, there was and continues to be an amount of phosphates that municipalities can dump. The 1972 agreement reduced the amount, but the amount continues to exist.
I'll try one more example. Suppose I started a new diet last week. I formerly ate all the red meat I wanted. Under the new diet I allow myself to eat only 100 grams a day.
The diet I started last week reduced the amount of red meat I am allowed to eat to 100 grams a day.
It would be wrong to say:
The diet I started last week reduced the amount of red meat I had been allowed to eat to 100 grams a day.
************************************************************************************************************** How can a agreement reduce something that has already been dumped?