90th for weight and 25th for height is a big flip in statistics, but remember these are just statistics! I think people put too much importance on numbers.
I freaked out for a few seconds when my oldest son when to his 4 year old check up (3 years ago). He had been 75th for height and 50th for weight nearly his whole life. He had flip-flopped to something like 80th for weight and 60th for height. And yet, you could see his ribs when he had no shirt on! He really did look like a skinny kid, so much so that I constantly encouraged him to eat! He'd been getting heavier, but not taller is all. I don't know where he put the weight, since you couldn't see it. Maybe he was adding density to his liver, and brain, and muscles, or something. Who knows! But technically, he was "overweight."
My 14 month old weighs 25 lbs. That puts him well above the 95th percentile, which I didn't even realize until I just looked it up. And he is the skinniest little thing you've ever seen. He only has a little pot-belly after he's stuffed himself at a meal. He can't keep his pants up! When people pick him up, they always exclaim that they're surprised he weighs so much. It's like he's made of bricks!
As a tall, not-narrow girl, I know how much emphasis is put on weight, and I learned to disregard it. When tv commercials come on and say how this one lady weighed a whopping 165 lbs until she did their diet, I almost laugh, because if I got down to 165, I bet my hip bones would stick out enough to hang a bucket on (that's what my grandma says she did when she was young--during the Depression). Again, weight is just a number!
I was also a chubby-ish kid, but not fat. Around your daughter's age, I probably looked a lot like you described her. And when I was about 12, I packed on weight. Part of it was over-eating, I know. But I had this unfortunate habit of pudging out right before a growth spurt. I would put on weight, look pudgy, and then suddenly I'd shoot up an inch or two without gaining any more weight. It was not fun during jr. high and high school. I wish I'd known what was happening to me. I only realized the pattern after I was fully-grown. If you watch her and see that happening, TELL HER what's going on, so she won't have this idea that she's yo-yoing.
I"m an emotional eater. It's not that bad at all, but I sometimes crave ice cream when I've had a bad day. I'm trying very hard to not do what my mom did, so my kids won't even have that little bit of extra temptation. I don't take them out for ice cream after they get shots, or if they've had a bad day.
Oh, here's something that I always thought was funny. My SIL is a tiny little thing, and she always wished she were built bigger. I couldn't believe it! But she loved soccer, and to really excel at it, you have to be built bigger than she is.
Frankly, she's so young, I would totally ignore it. Don't make a big deal about it. Listen to your mother's intuition, not your pediatrician. They don't know best every time. They have to compare your kid to other kids to do their job, but you don't. You have the time and energy to figure out what's right for your ONE kid. They only have a few minutes a year! I would only deal with issues that she brings up, to help her have a healthy body image.
And finally, I love that in Brazil, they call people who are built like me "strong." Not heavy, not wide, not big, but strong. Muscle weighs a lot more than fat does. I am, I think, quite strong. I am nowhere close to as fit as I used to be, but I still move my furniture by myself. Just the other day, I pushed two extra-wide, solid wood, glass-shelved bookcases, fully loaded with books, over a few inches because they weren't centered on the wall. If it comes to that when you're talking to your daughter, tell her that you bet she's really strong, and emphasize the advantages of that. Anyone can learn to be happy with their body type.