So I have a hard time accepting that whatever produced the incredible coordinated functions and variations of living things has to resort to such trade-offs in dealing with disease, or explaining how so many genetic diseases keep occurring, if the ToE is correct, and evolution really is the amazing system that brought about all the amazing perfections that are obvious despite the errors.
If ToE is true and genetic variation is created (more or less) randomly, then we would expect to see “trade-offs” such as genetic diseases. Coupled with our knowledge of how genetic material is inherited, a total absense of negative mutations would actually be evidence AGAINST evolution.
Or, is it possible too that there is a kind of "mutation" that IS beneficial, that is in fact normal or natural or part of the normal way things reproduce, that is predictable?
Anything's possible. But if you want to show this scientifically, you will have to offer some positive evidence that this is actually the case - mere speculation is not enough.