An important difference that people are overlooking is that the 2000 is made from red brass while the 2040 is made from yellow brass. Of the two, the 2040 is going to cut through the mix better (here is a page that describes the different brass alloys used in musical instrument production:
https://www.normans.co.uk/blogs/blog/difference-brass-finish-make-musical-instrument). All of the currently existing 2000 bridges were manufactured using a bridge blanks that were cast when John was still manufacturing bridges for PRS. That is why the model sports NOS (New Old Stock).
For those who are hesitant to purchase the 2040 because of the branding, I too was initially turned off by it. However, it kind of fades into the background after the guitar is setup and strung. I do not know why John chose to brand the bridge plate on its face instead of on the back like other manufacturers do, but I suspect that it is due to IP protection, so that no one mistakes it for a genuine second generation PRS trem (it is higher quality than a Gen 2 bridge). John more than likely holds the rights to manufacture the one-piece bridge without infringement.
Here is my 2019 translucent scarlett CE24 with the 2040 trem installed: