the board in the middle uses the pins from the side while forwarding the end IDE pins to the screen right?
At first I thought that too, that the LCD board used the end header on the Mega, but it doesn't.
The LCD board has a 40-pin connector that just happens to look like the large connector on the end of the Mega, however I think it plugs onto their adapter shield.
From what I can see that adapter shield uses all of the standard Arduino headers but not the extra Mega headers. Therefore you have access to the extra Mega headers which include the i2c pins and about 30 other general-purpose IO pins.
It' a bit confusing but I think you are good to go.