The problem is you can't practically do that for many compounds either because of ethical reasons or because it would take far too long and would in the mean time impede progress significantly.

Take plastics for example, they're as acutely non-toxic as you can get you're not having any readily measurable adverse health outcomes from handling it, touching it, and even consuming foods directly in contact with it. And yet there are still things we would have missed even if we adopted this whitelisting approach. We would have never captured the problem of microplastics that we see today, the mechanical and chemical breakdown of plastics in the environment leading to far higher consumption and presence of it in our bodies could not have realistically been studied or predicted even if we took a whitelisting approach.

Now you have to consider what the effects of whitelisting everything would mean for productivity and progress. Imagine how much more everyday things would cost if plastics had to be whitelisted before being allowed in any products. Even now knowing about the existence of microplastics, it isn't clear that the effects they have decisively outweigh the benefits of plastics.