I think training and experience may also play a great part in being able to present line - I've noticed that for instance when comparing videos of Lopatkina. There is one of her as Myrtha very early in her career, in the mid-90s, and although she of course already had that beautiful body with endless limbs, she didn't seem to control them as completely as she does now. Therefore, her legs in arabesque or her arms might be gorgeous on their own, but on the whole her line was lacking something (not much, but still...). It's not the case in later recordings - every movement is so organic it makes for an ever-flowing line that is mesmerizing to watch.
At the same time, I guess Agnès Letestu would qualify for "wonderful proportions and lines" on paper - but somehow, when she moves, there's always something that breaks the line for me (broken wrists, stiff back - although she can be wonderful in some roles and somehow overcomes this when she dances Odette, maybe because the swan arms are not strictly classical). I guess IMO she has lines, but not line, if that makes sense... And perfect lines may depend on changes in aesthetics, but I don't think line does.
Likewise I can think of the opposite situation - a dancer who does not have perfect proportions, but who has something that makes up for it - a way to present the movement as a whole, perfectly shaped. It reminds me of a debate I read over Evgenia Obraztsova's debut in Giselle, some people stating that her legs were just too short to ever be able to create the illusion of a spirit, whose lines should seemingly dissolve themselves in the air, and therefore be as elongated as possible. Several great dancers of the past had much shorter legs that is the fashion now, so it would seem to me that it's all about the way of presenting the choreography. There's a short video of her debut on Youtube where we see Obraztsova going for a 180° penché in Act II, during the famous sequence of slow developpé/promenade ; well, of course her lines will look too harsh this way, especially if her legs are short... The right romantic arabesque, with the upper body tilted forward and continuing the line of the leg, would seem to create the right feeling when carefully done, regardless of the dancer's height.
Same could actually go for Swan Lake 40 years ago, as someone said, but it's hardly the case anymore. It goes back to the debate over emploi (cf Diana Vishneva's attempt at Odette/Odile), but the ballet was not meant to be "Slow Lake of the Freakishly Long-Limbed" in the beginning after all...
(I hope no one minds my using precise dancers as examples, I mean no disrespect to their work - just some general thoughts they brought to my mind !)