Yeah I probably should go back and read the manual, DUH.
Anyways I actually got in contact with Jamie from BoostedNW, to make it easier I'll just quote his email in here,
So the chip is the way its supposed to be, there are no missing connections. The chip doesn’t read in that burner likely cause its not a chip in its stock form, it’s a modified setup for the function of the 2 timer itself. Pin 1 is not supposed to be connected, even on old style 2 timer boards that take DIP chips the pin 1 is bent out of the way so its not connected.

There is definitely not anything wrong with the 2 timer, we developed those many years ago, the design hasn’t changed, and thousands have been sold and used.

The chip being off, is likely the offsets not matching in that burners program, our guides are for our burners, and the way our software works with the burner. Not sure about the other software and the correct method to get it to burn properly. But even minus the 2 timer, if you have a 512 K chip, your putting in a car that normally takes a 256K EEPROM, you have DOUBLE the size, therefore the LAST half of the chip is where the tune will be read from. Thus the need to offset the tune to the 8000-FFFF portion of the chip.

a 256 k chip full range is 0000- 7FFF, a 512 k chip full range is 0000-FFFF (8000 is the middle).

So using a SST 27SF512 the offset needs to start at 8000 and end at FFFF. (for tune 1)

Then the 2 timer uses the extra pin (pin 1) which is actually EEPROM Pin “A15” the highest address pin, and when you ground that pin, which is what the 2 timer does, the chip then appears to the ecu as half the size cause its missing that address pin.

So to the ecu it then reads the 0000- 7FFF, as that is all it can see anyway, and that reads the “second” tune.
So the pin "missing" is the way it supposed to be as I had guessed. I will read through that manual and see what I can find.