I think if there were "divine engineers" that were designing new species
for the Earth, then they would (a) start with the simplest possible lifeforms,
perfect those, then go onto designing more complex lifeforms, and (b) each
new species would be based on a previous species, thus reusing previous,
proven technology, similar to how human engineers design cars, etc.

Whether new species are the result of random mutations or divine engineers,
there's simply no way to know.  People generally believe what they want to
believe.