The problems being discussed arise not because of biology, nor because biological organisms are not directly designed. The issue is replication with variation and the necessary historical consequences of this. The only way to avoid the consequences would be to stop replicating or to stop the variation.

The variation cannot be stopped, since no two physical things will ever be exactly alike. And if the replication is stopped, the whole system will go extinct, since no particular individual physical object will last forever. There is therefore no way to avoid the consequences of evolution: they are not biological consequences, but consequences of the laws of physics and logic. There is no way around them.