10 years of VLSI semiconductor design and fabrication, primarily II-VI and III-V but also with some Group 4 experience. I have a master's degree from Stanford in Materials Science and took graduate level courses in semiconductor physics and semiconductor device fabrication. I also have a master's degree in Optical Physics from the University of Arizona.
The size of the die is irrelevant. The mask set (i.e. the schematic of the chip itself) is almost certainly identical between the two suppliers.
It is possible that one chip could run hotter than the other chip. It has to do with the lateral doping profile and transistor geometry and a bunch of other things which probably are different between the suppliers. Of course that's also true for chips from the same supplier. How much different, no one but Apple could know. It could be that they're so similar, the performance is identical. Without a direct statement from Apple, it will forever be idle speculation.