If a transaction has two outputs, each to a different address, then only a script that uses the correct keys for both can get both.
Thus, you can control how much of the value there is output by a script simply be your choice of whether to supply that script with the correct key for one of those two addresses, or the other of those two addresses, both of those two addresses, or neither of those two addresses.
If a transaction has 100 outputs, each to a different address, then you have a much wider number of combinations of the outputs that a script can choose to take (as inputs to itself).
So, a script can control the amount output from a transaction, but, it is the scripts taking those outputs as input that do the choosing of how much value it wants its inputs to output to it. (The outputs it does not want to take right now, it need not take. The total amount of the output that can ever be taken in total is constant but the amount output at any given time - meaning, the amouint output to any particular new transaction that chooses to take some of those outputs - is set by the scripts of the transaction that causes the output to actually "happen", as it were.
The confusion seems to have been between the "potential eventual output possible if the right keys ever turn up" and "the actual output that ends up having happened by the time the universe ends or som other event ensures that not key that hasn't yet shown up will ever show up.
So what scripts control about the poutput values is whether they ever are output or not. More smaller "potentially eventually claimable outputs" means more "granularity" of the amounts scripts can eventually set in the blockchain as having been actually output so far, the remainder being possibly simply lost-forever coins rather than ever turning out to output to an input.
(If you only want half the amount to be output, you give the transaction two outputs and only give the key to one of those outputs to some later transaction that takes the value from the previous transaction as input. If you want the whole amount to be output, you eventually provide both keys, either both in one transaction or if you want the entire amount but half at one time half at another, you provide one key at one time and some other time eventaully you provide the other key.)