my personal opinion is that most of those people with "naturally toned bodies" are really minimizing the work that they do to get it it [ie, they work out two hours a day and tell people who ask that it isn't really much or that they don't really do anything special] or are just insanely active people. there is some amount of genetics in there, but toned to me says lifestyle factors.
if by "toned" what you really mean is very, very thin, then there is more genetics in it. but every shape can be toned imo.
and it's not just diet. it's lifestyle as well. it's the what the person eats, it's how much they just move around, it's how and how much they work out.
diet is a big factor in weight, but diet alone doesn't do a thing for your making your muscles visible. that comes from using them.
-google first. ask questions later.