Notably, appeals to not having your phone on in an airplane and airplane mode are more due to the extensive reach of an airborne cellphone and the effect this has on cells and hand-over protocols, as the phone connects to a plethora of cell towers in rapid succession, by this seriously harming available capacity. So this is intended more to protect the earthbound infrastructure than the cockpit electronics. I'd guess, subverting any countermeasures by means of the baseband system would be contrary to the interest of those involved and profiting from this.