You're absolutely right. Technically, anyone with enough knowledge can interact directly with Thorchain or Mayachain. But in practice, doing so safely and efficiently is non-trivial. We've seen many cases where even technically capable users lost funds due to minor mistakes in transaction crafting.
NativeSwap is for general user or even for technical person if they want to ditch manual crafting in exchange of little fee. And that is the main motto of NativeSwap, making cross-chain exchange cost effective
That said, if you're comfortable working directly with the protocols, there are definitely alternatives available. Our focus is on making it cost-effective, easy and secure for general user.