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Speciation is what you are looking for. The idea is that both the lock and key in your analogy gets shaped over time through the processes associated with evolution.
If a sperm from a different species (example – lion) fertilizes the egg of another species (example – tiger), it may form an offspring (liger). But there is no guarantee that it could create offsprings if it were to be bred within the liger population. But over time, with evolution and natural adaptation, the species can either attain their fitness or go extinct.
But naturally, speciation occurs when a population of a species gets separated and a genetic drift occurs. For example, if they get separated geographically when they are in isolation, the population could develop traits and variations in their genetic structure over generations. And through natural selection, they diverge into an entirely new species. This is known as allotropic speciation.
This could happen even without isolation too. They are called sympatric speciation and they happen due to various factor causing a genetic drift within a population.
When you take the time into account, the diversity in species would make sense in the evolutionary sense.