With the way you are describing things genetic diseases would never be a thing because they would be "phased out".

I literally know nothing about these exact proteins, but just because something is better at making a microorganisms reproduce billions of years ago doesn't mean it's the best for us today, just it's still good enough not to have given us a reproductive disadvantage. It also doesn't mean it's the best for us as modern humans. We have shittons of defects that might not matter too much in terms of evolution, but is something we definitely would love to get rid of as humans.

Another good example of how the motto of evolution is "good enough" is oxygen. Our cells are literally constantly poisoning and damaging themselves with oxygen in order to produce energy to function, but it works well enough for us to reproduce before we get too fucked up and die.

I see what you're saying, but look at it this way, sometimes medical researchers find new uses for old drugs, some that were even harmful in certain applications (eg thalidomide), so it's possible an archaic protein could be useful, and not dangerous.