Are you serious? You don't think the people in physical possession of the part would have noticed rubber or neoprene and commented on this? Instead, they specifically commented on the milling marks.
Have you never held a piece of machined metal in your hand, rotating it and looking at it from different angles to see how the light plays off of it, creating the illusion of raised and lowered areas?
The marks are left there on purpose. My belief is that Apple plans on gluing the battery and other components onto the case. This was doubled as a surface preparation in order to achieve a good glue joint. You can see that the areas where there will be nothing glued to the case are nicely polished. A polished surface would not at all be suitable for gluing.
The following is from Ifixit's teardown of the Macbook Pro:
Someone really did not want the battery in the MacBook Pro to come out of the upper case. We tried valiantly with our iFixit 6 Inch Metal Ruler to free the battery from its aluminum confines, but to no avail. Rather than risk puncturing a lithium-polymer battery cell, we left the power source in place.
And the following is from an article on the subject:
What's more Retina MacBook Pro's battery is glued into the computer. This increases the chances that it'll break during disassembly, iFixit said. Further, it covers the trackpad cable, which increases the chance that removing the battery will shear that cable.
In fact, the Retina MacBook Pro's battery has been glued into the case so strongly that it couldn't be freed, according to the company. "Normally, we're happy to unglue things, but this was different," iFixit's Wiens said. "We were pretty intimidated by the amount of glue we found on the battery."