The native ports have additional features, which are easy to implement starting from the native compilation. For example, the native port of Zelda has gyro aiming and automatic autosave options.

Well I was hoping there'd be a way to translate mouse input into the joystick input in a straightforward way that isn't available on emulators.

It could be done with native mouse control. No joystick intermediate- instead modify the C code to allow direct control of the player character with a mouse.