The factory has a lot of freedom as they license the brand but are responsible for all the rest (making, selling, distributing etc)
Why do you say the current board is a 2layer board?
At the beginning of the production process there was a delivery problem related to the oscillators and it was decided that we wanted to ship anyway as that functionality was not supported by Arduino. Sometimes tradeoffs have to be made in order to deliver. Other delivery issues have impacted on the ability to ramp-up production.
Different batches are shipped to different distributors and they appear on the market with not so predictable patterns.
Effectively this is all done on purpose to give something interesting to do to the people who like to play sherlock holmes on the forum (joking...) 
The board is open source, the files are released as a "reference design" and they have very very minimal differences with some batches of products. When the production stabilises we then put online the final design files.
Stating that this board is not really open source because there might be very minimal differences with one specific batch of products is really disrespectful of the amount of work that arduino has done over the years to develop the open source hardware market. We never had profit as out first driver and we have given away a lot..
Others are bailing out of being open in order to make more money while we're still here doing things like the very first day.