Mech Engr who works with fasteners and things that are assembled. Its my life's work!
Alternate screw recess designs are possible; 5-lobe like found on the iPhone, Torx Plus, Nacro, 00 or 000 Phillips, and MorTorq Super MTS-04 micro screw. Each design offers certain drive system strength capability but limited by head thickness and minimal thickness of the components being fastened together. Secondary function of the recess is to provide some level of tamper resistance as driver bits are not readily available.
The screws appear to be MicroStix 3ULR and referenced here www.j-osp.com/en/products/neji.html. The micro screws are patented by OSG Japan. As jrehwin mentions, they first showed up in Hitachi and Seagate 1" hard disk drives then later in MS Zune player and gaming systems. Licensed to Unisteel Singapore. Source for licensed bit manufacturer is unknown.
Given the quantity of Apple watches to be produced and the volume of screws needed to meet that demand, the screws will have to be formed, not machined. To deliver torque, the slanted 3-lobe recess design works with minimal depth providing enough strength for adequate clamp load. The difficulty in making and forming the screws lies within the very thin head and depth of recess required. The blue material shown on one of the screw threads is a chemical patch. It works as an adhesive to prevent vibrational loosening in very short threads.