However, in many amateur pictures taken in the H-alpha wavelength (like in TFA), the artistic choices come into play, as you said. In the Simon's first image the prominence layer (just outside the limb) is shown as-is (positive), while the disc interior is shown inverted (a negative; note e.g. how the sunspots became white). This is done to get a somewhat more "3D look". In a normal, non-inverted image, the mottles and filaments show up as dark features on a bright background, while inverting may make them look more "natural" (to some) - sometimes downright "casting shadows" (a solar filament often has a brightening around its base - which becomes dark after inversion).
Source: I'm the ImPPG's author (and enjoy solar astrophotography myself).