The measurements for the positions are not from the end of the boom....they're the distance from the reflector. Look at the 900Mhz antenna specs just above the 1.2Ghz specs on the sheet and you'll see that the reflector is at 0". On the 1.2Ghz table, the spacing of the columns is off because D8 has no value.
Regarding the overall (folded) wire length of the DE, I don't think it matters that much; you just want the finished width to be exact. Since the author says that you can use any diameter of wood, the placement of where the coax is soldered could also change. If the overall length mattered much, then the coax placement would be critical, too. I looked at several other variations of this using the complete folded dipole approach also. Ideally you would have an SWR meter to check it and trim the other end anyway.