Leggings are so in style it's not funny lol. Leggings by themselves is a no no. Not only is it a fashion no no but leggings are tight so putting a normal shirt with leggings does not look "classy" and with little kids obviously you don't frown at them. You frown at the parents lol.
Leggings under shorts would be really cute. My rule is the shirt has to a bit below her butt when they go under tunics. I love getting bike shorts and having them go under skirts and dresses. My daughter is 2 1/2 in 3T but I notice some of them don't have built in shorts and I want her to have something so her diaper doesn't look saggy even if it's empty lol If she was older I'd do it too so she didn't show her underwear when playing.
You are right on target with the shoe match up. Capri leggings look better with flat. Depending on the boots, it may look good but I don't know. If you pair shorts obviously they can't be capri length or it would defeat the purpose but if it's too short you'll get some looks. So I would say mid thigh, kinda like the shorter version of bermuda shorts.
I am ocd about colors, but the leggings have to match in some way to the shirt or shoes. If they are striped then the shirt can't be striped or anything, but if yellow is the color that strands out in the striped leggings she will wear a yellow shirt, see what I mean :)
I would check out sales if you can, I don't think you can stretch out clothes that are too short :P