Ahh, symbolism.

Getting a cutie mark while crying? What a cruel joke the universe must be. Alex doesn't understand why this of all things would trigger him getting his cutie mark. What does it mean? Why now, at the then current worst point in his life. He'll never be able to tell this to the other foals at school, it would just make him cry again. He doesn't even have a cool special talent to make up for it. All the other foals at school are doing stuff like specialized magic spells, crazy flight tricks, bringing plants back to life, all Alex thinks he's good at is being sad.

Well, while he doesn't know what it means or why he got it now, some day it will all be clear, and may even be clearer to others sooner than he thinks. He did not get his cutie mark from crying, no, that triggered him getting it yes, but it's actually the reason behind why he's crying. It's his emotional openness, his empathy, his heart. He has a level of affection and empathy for others that he couldn't even dream of, and even within his future vices and issues, his heart never fades for those he cares the most deeply about.

He does not have a flashy or even very visible talent, but it is a lot more important and impactful than he could ever give himself credit for, and it drives his very soul for his entire life.

It's just such a shame someone had to die for him to realize this at such a young age. Bittersweet.