The size of my confusion is "second to none"

Why "second to none" is being considered as "the best" instead of "the worst" (almost non existent)? To my understanding - "none" is "nonexistent", while "second to none" should be... well... almost nonexistent.

To be second to none means that nobody is ahead of you. None is nonexistent, which means that someone nonexistent is ahead of you — nothing better exists, so you are the best.

This dates back to the Coldstream Guards

The regiment is ranked second in the order of precedence, behind the Grenadier Guards. This is because the Grenadier Guards have served the Crown for a longer period of time. However, the Coldstream Guards is an older regiment, and because of this, has the motto Nulli Secundus (Second to None). The regiment has been referred to as the "Second Regiment of Foot Guards" in Parliamentary state papers,1 but this term has long fallen into disuse and was never used by the regiment, hence their motto. When parading with the other four regiments, is always on the extreme left of the line, with the Grenadier Guards on the extreme right. This ensures that the regiment is indeed "Second to None".

Think of the meaning of the following sentence (modeled off your title):

The size of John's house is second to Jane's house.

While John's house is (presumably) quite large, Jane's is larger.

The size of John's house is second to none

says that there is nothing to which it is second (so it is first).

Second to none could be used to mean the best, the worst, the fastest, etc.