But you could say that whale flippers are 'basically' their hands.

Every scientific model and analogy is flawed in some way, but many are still useful.

How exactly is this theory useful? Yes, frogs and humans process visual information because they both have eyes. That’s about all those structures have in common.

For nearly all of human history everyone thought that those frog vs. human eyes were completely separate and designed by some magical being living up in the cloud.

By noticing that while they have significant differences, those structures also have significant similarities, we were able to correctly answer one of the greatest questions of all time: where did humans come from?

Of all models, this one is particularly useful.

To be useful models must accurately represent some aspect of reality, Reptiles don’t seem to represent the brain of our common assessor particularly well. So this model is as wildly wrong as describing volcanism as the bowel movement of animals. Yes, they pass significant material through a small opening, not it’s not a useful model.

As I have mentioned before these structures are very different, compare the giant spheres used by snakes, bird, frog etc to process visual information and try and map that to a rodent, bat, or human. Hint you’re not going to be able to locate an obvious sphere because the fundamental morphology is just different.

Eyes are a good example of conservation and path dependence, development is initiated by a fairly highly conserved gene:

https://en.wikipedia.org/wiki/PAX6#Species_distribution

Being reasonably conserved has minimal predictive power. Yes, knocking it or a closely related gene out out harms eye formation in a wide range of species but it says little about what specific structure ends up being formed.

Putting this particular theory aside the generalization that evolution is a nested hierarchy of structures is pretty obvious on the macroscopic level. Traits like breathing oxygen, having symmetrical bodies, backbones, limbs. These are all examples of structures building on top of one another sequentially and conserved across species. Sure each of these subcomponents continues to specialize but the core functionality remains largely the same.

Going back to your analogy saying visual cortex of frog is wildly different from a human visual cortex. That's similar to saying a frog backbone is wildly different from a human backbone. Sure that's true but there's also a shared common core functionality largely conserved across time

Again the issue is the theory is misleading. Those traits are conserved through evolution largely because their useful, but if you look at say owl skulls you find while asymmetries because that’s more useful. Hagfish lost backbones and snakes lost limbs because nothing is sacred to evolution.

So yes frogs and humans both have a visual cortex, because we both have eyes. It really doesn’t explain anything beyond that point.

I think taking a macroscopic view like this points at interesting types of analysis. Evolution is analogous to a hill climbing algorithm navigating towards local optima in a probability field. Macroscopic evolutionary trends give a low resolution peek into the underlying probability distributions.

That’s not what this theory is suggesting.

Frogs, birds, etc have very distinct spherical visual cortexes. Humans and squirrels don’t have that kind of spherical structure. So, other than naming where vision is processed the same thing the overlap isn’t particularly strong even at the most basic structural level.

It’s perfectly reasonable to extrapolate from studied organisms to species that share recent common ancestors. But reptiles don’t represent the probability distribution, they represent different results from that distribution under different evolutionary pressures. Extrapolation backwards and our common ancestor was very different from all decedents.