First of all, halflings aren't half anything. They are a race in and of themselves. They aren't half elf and half dwarf or something of that nature.
Second, Charisma is also natural charm that someone has. What a boost in Charisma implies is that certain races have more natural charm than others. So, a halfling is seen as more charming, possibly cute and adorable by other races. A half-elf is considered more attractive and charming than perhaps a typical elf or certainly many types of dwarves.
And I wouldn't say that casting a fireball spell with Charisma as your bonus is you intimidating Mystra. It's more like the spellcaster's influence over the Weave - which is like the Force in Star Wars. It is kinda sorta intelligent by itself, and is sort of a part of all living things. It binds the galaxy together.
I mean, not exactly, but kinda.
The point is, someone with high Charisma is someone with a good amount of charm, or they know how to speak well in order to influence and inspire other people, animals, spirits, etc. Or they carry themselves well - like someone who walks down the street with an entourage and you just sense they are important. They don't even need to speak. Their very presence just emanates from them.
It CAN be intimidation as well. It CAN be like Darth Vader who simply appears on the battlefield and melts the hearts of his enemies with sheer terror. It CAN be like Jabba the Hutts laugh that makes your heart drop into your stomach.
All these things are Charisma, and it is not abnormal in RPGs to have certain races have greater Charisma than others.
