Sorry i'm having a hard time understanding, could you maybe give a more concrete example?

Like when you said " In biological systems the strongest tests we have are transgenic organisms in which a single gene can be knocked out, but it is never clear even here that differences in trait value are direct effects of that single gene, or whether the knockout has downstream effects arising from cis-regulatory differences in the gene pathway or any other indirect effect." So you have a hypothesis that some scientists have developed, that gene x causes y, so you run experiments and conclude that "knocking out gene x does appear to cause y, although the exact mechanisms for this process remain uncertain" This conclusion leads you to understand how you can effect y, without making assumptions about the details which you are not aware of. Why is this approach less useful?