so say i shoot a dude an NPC with a pistol in short range, that's 1 difficulty in normal conditions.

If I shoot the same NPC in short range with a magic attack, is that 2 difficulty because of the rule of increasing difficulty with magic or does it not affect combat checks?

A basic attack spell is easy at short range.

The increased difficulty applies to narrative checks outside of the listed spells, like trying to break a door down with magic instead of with an Athletics check.

Basically if you’re in combat look specifically at the second section of Spell descriptions. If you’re out of combat then treat it just like any other skill check, the gm setts the Difficulty based on what they think the task requires, this is where magic is always 1 dice harder.

This is also where things like flight (Augment) and mind trick (Curse) come in. Those abilities don’t have specific rules for a structured combat encounter, but out of combat the gm just sets a difficulty and away you go.

For flight as an example, perhaps you are flying onto a roof, normally it would be an Average Athletics Check, therefore it’s a Hard Magic Check