2. he was subject to Encom parallelism laws. He had become an in-computer “echo” of the spiritual energy of the Apple corporation. he was following their exact same aesthetic change from “80’s rainbow” to “2010 glossy white and silver.” The appearance of literal shiny chrome apples was an omen (signaling that his “mirroring” had become close enough to weaken the veil between worlds, making it possible for Clu to send the page and Sam to enter)
3. Tron kept giving him the silver apples. Tron had learned about both 1. classical mythology and 2. Olympic medals. The gift signified “to the second fairest of the gods”
(…these could all be different theories. But they also could overlap. The manifesting of apples in echo of Apple could coexist with Tron (zler) always being the one to find them and sneak them to someplace where they’d end up being brought to Flynn.)
(And Flynn could be totally oblivious to either of their true meanings, and view them as just reminders of the orange …let’s be real, after a few centuries in the computer all roundish fruits probably start to look the same. Especially ones that just take on the color of whatever’s nearby, instead of being actually red or orange themselves)