The notion that the human brain imprints itself into the electronic world works well with the idea that programs have an appearance based on the people who wrote them. In the original film we might imagine that "generic" programs, like the many duplicate security guards, were originally written by one User at Encom and then simply copied however many times due to the nature of their deployment.

From there, Flynn's Grid, which is populated by MANY programs not visually related to Flynn, seems to operate under intentionally different rules. It's noted in production materials that the average program in the Grid is referred to as a "Basic". It insinuates Flynn realized he had to devise a way to populate the Grid without the benefit of thousands of existing programs from thousands of programmers, so wrote a "basic" routine to generate entities.

Clu 2.0 meanwhile, is more like Flynn's attempt to take control of the way a program looks like its creator, going much further: making Clu 2.0 a full copy of his mental patterns, not just a sympathetic likeness of his appearance and some of his personality.

The GRID is an Alternate Parallel Universe. An Alternate Reallity. A Digital Frontier.