I think it was supposed to switch to color when the Matrix was shattered, showing that the world changed. Sort of like how it went from black and white to color when Dorothy arrived in Oz.
Those seeker alt modes look super neat, I love the slight but characterful distinctions between them. Really hoping we see protos of them soon.
Because it is Manga, not a comic. The color bit was just for the western influence but the entire run will be done in Manga style. Like any good Japanese company would do.