Help! I have issues understanding some IGCSE principles.

No you won't get penalized for either. You just won't get a mark for them

The grade boundaries vary each year depending on the difficulty level of the paper and how the students perform, overall.
Like, last year many students for maths got 200/200 and the grade boundaries went way too high and our grades fell pretty badly

Um well that honestly depends on the subject. If you're gonna continue that specific subject in the future, then yes, it kinda ruines your results. But then (god forbid), say you fail in Physics but you have no plans on continuing it in the future, that really doesn't matter.

Hope I cleared your doubts, any more doubts please feel free to pm me