Lisa's not actually that much taller than Sarah, but she is wearing tiny shoes, and Sarah is not. Amanda, meanwhile, is just very tall. I mean, technically she's not at the moment, but... You know what I mean.
This is something I've addressed outside of the comic itself before, and something I get asked periodically to this day. Color adds complexity in simply having more to keep track of (and having to add white to more characters eyes), but isn't too bad if you have a palette sorted out.
Sorting out the palette, however, is the real problem. Characters are challenging enough, particularly when there are extras, but it's backgrounds and objects that really makes things difficult for me. I underestimated the challenge the overall composition posed back when I brought color into Squirrel Prophet, and while it could be fun and rewarding to work in color, it was horribly impractical for sticking to a schedule, and I likely would have stopped using color mid-storyline if not for the fact that almost everything was happening in one location with a reusable palette.