Applebloom's construction and potion-skills are things she's learned as is Scootaloo's riding. Sweetie's music is a natural aptitude. However a True Talent is a combination of these with the pony's mindset and what brings them happiness. It is a particular path and a particular set of goals that bring them the greatest personal fulfilment. So, whilst all three Crusaders have diverse skills and likes, there is one thing that really brings them joy and that is helping other ponies find their destinies. Ergo, their cutie marks: Knight's shields, created by their own subconscious 'Crusader' ideations, with unique devices on them hinting at their personalities, aptitudes and personal approaches. Even more interesting, cutie marks whose colour scheme is all three characters' mane colours - indicating that their friendship is so strong and so binding that they will only find true personal fulfilment in working together.
Some examples from the Mane Six: Look at Pinkie Pie. She's a great baker, has reality warping powers and is a gadgeteer; she's also got a wonderful sense of humour and has an enormous talent for organisation. Her cutie mark reflects none of these things. Rather it shows that she's happiest when she uses all her skills and aptitudes to make other ponies happy. Rainbow Dash is another example - She's a skilled flier and weather engineer; she could have any career based around flying, civil or military and do well. However, it's only by being a flashy, public-wowing aerial acrobat that she'd find real happiness and fulfilment. Some might call that 'shallow' but the point is that True Talents naturally express the whole of the pony's personality, good or bad.
As for the atypical light-show when they got their cutie marks? Well, these are the personal students of the Princess of Friendship, after all. They even have been the beneficiaries of the personal and unusually in-depth attention of the Princess of the Night in their dreams. Yes, there is probably something special about those three although whether that is ever specifically addressed will probably at least in part depend on what the writing team do next with the characters.
The Meaning of the Marks
In General: Knight's shields is an obvious reference to 'Crusader' as well as symbolising the ancient concept of chivalry and helping those who need help. The colours show how this is their joint destiny and that their first, best talent involves them working together.
Sweetie Belle: Musical note in a star - As well as referring to Sweetie's singing talent, it is also a reference to her more subtle ability as a motivator. She understands what makes ponies tick on a psychological level and can help them untangle the knots of their own thoughts. Although her cutie mark mostly applies that to entertainment, this subtle magic of the mind (as Trixie exemplifies in her own way) can be one of the most effective helping tools to have available.
Applebloom: Heart with an apple - As well as referencing how important being a part of the Apple family is to her (that's an anxiety she's expressed on several occasions) it also shows the degree to which her understanding of the world and her problem-solving comes from her understanding of ponies in their social groupings like family; she even treats a foreigner like Zecora like family!
Scootaloo: Lightning bolt within a wing - Scootaloo has always been the one who's wanted an 'awesome' cutie mark. She's fearless (at least outside of her own social anxieties) and in love with speed and agility. When solving a problem, she's the one most likely to come up with a solution that's amazingly dangerous, showy and, as always, awesome! Because how else wouls she face Rainbow Dash?