A big connector with lots of NC pins is used to provide mechanical stability: this connector is the only thing that holds the RPi and the display together. A smaller connector could easily unplug, and the rigid HDMI connector would then badly damage the HDMI ports on your RPi, the display, or both.
This HDMI connector also makes it impossible to use GPIO splitter directly: you need to keep your RPi at a fixed distance from the touch-screen for this link to fit.
Basically, if you need access to GPIO and a touch-screen, the best solution is to buy a touch-screen which connects to USB. This has the advantage to work with any SBC, not only Raspberry Pi. However, if you want to use the touch-screen you have, you'll have to use a short HDMI cable instead of the included connector, and make GPIO connections either using a splitter or jumper cables.