The EAGLE file is also public domain.
That's why they all have the same layout. Why go through a bunch of work to change it when you can just slap your logo on there(or the Arduino logo for the counterfeiters) and send the gerbers off to the board house? Cloners and counterfeiters want their product to look just like the official Arduino board because that's what the buyers want to buy.
That said, there are some different designs of clone Unos. Most use the CH340 USB chip. I have one with through holes next to the female headers, a useful improvement!
Of course many of the companies who sell the Uno clones/counterfeits are outsourcing the manufacturing to board printing and assembly houses so there is a good chance that many of these boards are manufactured at the same factory but the same schematic and gerbers sent to two different factories are still going to look almost identical.
arduino.cc doesn't manufacture their own boards, this was previously done by the .org people but since the split .cc is contracting the manufacture of their boards to various companies in different countries. If you read the Arduino blog they post whenever they get a new manufacturer. The USA manufacturer is Adafruit, The China manufacturer is Seeed Studio, etc.
Are you 1000% sure that Sparkfun actually manufacture the Arduino?
I've never heard anything about Sparkfun manufacturing the Arduino Uno. Their product photos of the SMD uno say arduino.cc made in Italy, the PDIP version says arduino.org but the last I had heard they were buying Unos from .org(SparkFun and the Future of Arduino - News - SparkFun Electronics). They have their own version called the RedBoard. https://learn.sparkfun.com/tutorials/redboard-vs-uno:
we manufacture the board in-house, here in Boulder, CO
They also manufacture the Pro Mini, Pro, Fio, and Lilypad. https://www.sparkfun.com/news/1791:
We’ve been building and will continue to build hundreds of thousands of the official Arduino Pro, Pro Mini, Fio, and LilyPad. The royalties will continue to go to Arduino.cc, the folks we license the US trademark from. Recently we’ve offered to license and manufacture the other official Arduino boards: Zero, Uno, Mega, Due.
look at their publicity photos. All boxes and shelves. Just like a distributor. No robots, CAD systems or reflow ovens. See any logic analysers for testing?
Here's some readily available evidence of Sparkfun's manufacturing facility:
If you need to see it to believe it you can go on a tour of their facility in Colorado, USA: About SparkFun - SparkFun Electronics
Of course it is possible that they contract some of their manufacturing overseas but saying they're just a distributor is definitely wrong.
Adafruit does manufacture the Arduino Uno in the USA: Hand making the first Arduino UNOs in the USA #TeamArduinoCC - YouTube