Interesting thoughts, thanks for the feed back. If you'd like to participate in more development/design discussion, feel free to join the discord.

There are a few ideas I think are distinct here:
1. The dichotomy of theoretical (things you know) and practical (things you can do.)
2. Organization and structure
3. The distinction between skill and proficiency

(1) Starting from the top, this is something that was a major decision during early development. The level of abstraction the proficiencies have is a bit variable, so some decisions are a bit confusing. For example, "basic science" is generally meant to represent an elementary school level broad understanding of the sciences. Advanced science represents a highschool/college level of broad understanding. Then, you have specializations that extend off it, which would be more representative of being an actual professional or expert of that specific subject. Each of these has a different level of abstraction.

Then, you have practical proficiencies such as crafting and construction. The earliest part of the tree is sort-of stand alone as you've suggested. Basic fabrication leads into the various crafting specializations. The problem with doing a completely separate tree, though, is that some practical knowledge reasonably relies on theoretical knowledge to make sense. For example, "basic mathematics" essentially represents the ability to count and do basic arithmetic. It'd be hard to argue that something like mechanics wouldn't atleast require a peasant's understanding of numbers.

I don't hate what you've described, but one of the core design decisions is that proficiencies represent compounding knowledge. Splitting the two would work from a gameplay perspective, but not from a logical perspective.
That said, I have been rolling the same idea around for a while trying to come up with a way to do exactly what you are describing. I'd love for research and construction to essentially use a two phased approach where someone with theoretical knowledge (lets say geology) has to sign off on the construction of a building before the builder can continue, allowing the builder to essentially know less on the theoretical side, but still gate the building behind the proficiency.

I think there's still room for evolution, but there's a lot to discuss.

(2) Partly discussed above, the structure of proficiencies is largely dictated by the compounding nature. You need to understand mechanics and physics before you can understand engineering, for example. And naturally, you can't do any of that if you don't know how to count.
There may be other ways to structure and expand the tree that would still make sense while also being more forgiving. For example, having different "tiers" of some proficiencies. Instead of basic and advanced, you could have several tiers of mastery for say "science" that represent the same broad body of knowledge on science subjects and processes. Different proficiencies could branch out of those sub tiers, so that there is a greater distinction between a practical specialist like an engineer, and a theoretical specialist like a scientist.

You would still have the tight coupling of the two "trees" of practical and theoretical, but there would be more distinction between the two, and sending someone down a specific tree would represent a larger commitment. The downside of an approach like this would be that it would make it even harder to patch recipes, buildings, and research topics, since you'd now have to think "Well, this obviously should require physics, but does it need a basic understanding of physics, or a true master of physics?"
I'd also worry that tiers like that might confuse the players.

(3) Skill and proficiency are already a bit blurry. I've documented the distinction as such:
Research: Knowledge you have access to (blueprints, plans, designs)
Proficiency: Knowledge you personally have (How to work with electronics)
Skill: How much potential you have, how good you are at doing something

Rimworld skill is already abstract. Every type of crafting falls under Crafting. Every type of building falls under Construction. While it certainly wasn't the original intent, with the introduction of proficiencies I have had to draw a fuzzy line between skill and proficiency to justify the latter's existence. To do this, I've rationalized it as above.
With that said, a common complaint is that a pawn spawns with high medical skill, but no medical knowledge. This is an unfortunate result of how Rimworld treats skills and how we choose to rationalize.
The ultimate result is that sometimes a pawn seems like they should know something because of how skilled they are, but don't because their backstory doesn't suggest they should.
In your specific case, it's almost certainly just because that race hasn't been patched yet.

Some have suggested either capping skill or awarding proficiencies automatically based on generated skill, but I think that would only further blur the line.