The scientific method does not make that assumption. The scientific method only assumes/requires that doing the same thing exactly the same twice will produce the same results. Everything is built on top of that.

> that our perception allows us to interrogate these properties.

That's not about science, that's about logic. Anything that can interact with people can be detected and interrogated. It does not exclude the possibility that other things may exist but there is both no way for us to interact with those things and, as such, they have no relevance to our lives.