Everybody seems to debating the hardware but to me the question is software. With this mean Apple's desktop software would become incompatible with the new arch

Everybody seems to debating the hardware but to me the question is software. With this mean Apple's desktop software would become incompatible with the new architecture? Also would this mean less control for for the end user on the laptop / desktop form factor? I'm picturing only app store from iOS on those form factors...yuck