Check out this page.
http://www.trek5.com/caps/tos/39_MM/pages/39_MM-013.htm
It clearly shows the higher domed b/c deck. Plus the yellow rectangle is a dead give away for the 2ed pilot version of the TOS-E. As for the other marking I to can find no shots of these markings in the final print of the show. I would speculate that it is an added touch to give the ship some more charater beyond the 2ed pilot version.
Given that the kit was sculpted by Thomas Sasser I would be hard pressed to question the acureatcly fo the kit. But you have to admit the declas are kewl. <grin>
As a intresting side note the same group of pages shows the ISS E from the rear and it has the bulb necel end caps of the series version.
http://www.trek5.com/caps/tos/39_MM/pages/39_MM-028.htm
rogue