they're generally just better optimized games.
it has to be accounted in nesmaker that the game engine is not exactly well optimized for ANYTHING, because it's designed to do a little bit of everything for every type of game.
for instance, your game is running 2 sets of physics engines on top of eachother at all times, which is a massive waste of processing power.
the main reason we've been able to pull off things like 4-directional scrolling and parallax without scanline counters and still maintained gameplay in dimension Shift is because we've spent a year optimizing the engine, removing parts of it, and rewriting
slow code to be less slow. For instance, if one would slap the scanline counting code we use into a vanilla nesmaker engine game, it would still work, but the game would run at half-speed at best.