Look. It's simple. The semiconductor business is a cut throat one, and Olympus has to order a sizable quantity to justify a production run. Otherwise, your Pen cameras will start having as much as a 10-25% price increase, or you will be stuck with the same sensor for a long time.
Asking for a new sensor is difficult simply because of the cost etc. Perhaps why Olympus is still using a 12MP sensor is because it has a huge backlog of 12MP sensors waiting to be used because they had to buy lots of it to keep the prices low.
The sensor has to be fabricated to the dimension required. You need pad outs and such for bonding wires out of them. Its not 'cut-able' to any size the manufacturer pleases.
If they just use AS IS which is APS-C sized, then the sensor cost is passed over to the consumer and the camera innards will need to be redesigned to cater for the larger sensor.