Yes, you are absolutly correct.
The reason for this is that living things are evolved, rather than designed.
We have seen that even in very simple hardware, when using a genetically evolved design, we end up having circuits that functions as per the requirement [1]. But it ended up being very hard to figure out how the thing actually worked, and when components were removed that seemingly did not have any purpose, the thing stopped working.
And this, in my opinion, points to a very important aspect of evolved systems. We can only have a statistical assessment as you say. But no way to say for sure that, "This and this alone will be the only effect of an intervention".
But we can have some idea, depending on the type of intervention. For example, we can say that something that was part of the evolution, will not interfere with its working, simply because evolution has taken it into account during the process. And here comes the concept of something being "natural" to the organism. So we can say that stuff that is taken orally, is much safer than injected stuff. All through our evolution, we have been taking stuff orally. So a Vaccine is much more like throwing a spanner into our workings, than taking something taken orally. Similarly stuff that were part of our natural environment, during evolution can be considered as safer, as opposed to stuff that were not.
I think this is why mocking the concept of "natural", by saying, "Everything is natural, because it is found in nature", is embarrassingly missing the point..
[1] https://www.damninteresting.com/on-the-origin-of-circuits/