By my title I mean for example time and skips differences. I play on the Nintendo Switch and I have noticed I have some loading zones up to 20 seconds. Will that affect my time in the Any% Console category?

Please see the rules of the category you are going to run: In Any% time is taken without Loads so no your Time will not be affected by those loading times. The difference between console and PC is that some of the skips (especially hunger skips) are easier to do on the PC Version because you can use Keyboard and mouse for it.

If you want to see further differences watch some runs^^