The question is:
Does Darwin imply that had there been no such similarities [such as between the hand of a man or monkey, the foot of a horse, the flipper of a seal, the wing of a bat], the only explanation would be a supernatural force?
We do see these similarities. We want an explanation for them. As Darwin writes, "if we admit their descent from a common progenitor, together with their subsequent adaptation to diversified conditions" then these similarities are "intelligible". He doesn't see how they would be intelligible otherwise.
The fact that Darwin does not see how they could be intelligible otherwise does not mean that a supernatural explanation would be needed if the descent description were not true. For example, those people who think we are simulations don't require a descent at all. All they need is a "posthuman" civilization willing to turn on a simulation. See Nick Bostrum's Are You Living in a Computer Simulation? for this perspective.
Furthermore, the descent itself is not generally problematic for theism. That is, theists do not require this descent description to be false for theism to be true. Theists need only add a metaphysical view that God guides this descent, however it may be described, and then there is no conflict with theism.
Atheists, of course, add the metaphysical view that nothing guides this descent and it happens in some way that does not involve such agents, perhaps no agents whatsoever if determinism is also true.
In both cases, theist and atheist, there is a metaphysical view added onto this descent description.
The descent itself is just a description. How that descent happens is where the potential need for supernatural forces can be introduced or rejected. Alvin Plantinga presents a theistic argument in Where the Conflict Really Lies. Richard Dawkins presents an atheistic argument.