It's a bit tricky but I'll try to explain. One example I'll give is that the characters tilt back and forth while walking. The characters themselves are 64x64 sprites, but these sprites are scaled up to much bigger than 64x64 before they are tilted. Were the game at a true 64x64 resolution, the character tilting would result in the induvidual pixels tilting. If you look at a game like nuclear throne or gungeon you can somewhat see what I mean in how weapon sprites are handled when held by a player or enemy and aimed in different directions.

This sort of thing also applies to some of the particle effects, as well as the lighting.