Adding div after every two post on main loop! Why will first post not get counted?

The first post doesn’t get counted because you have this in your if statement:

0 !== $wp_query->current_post

According to The Codex on WP_Query:

(available during The Loop) Index of the post currently being
displayed.

Being an index of the array, arrays always start off at 0 as it’s first item. So by having that in your if statement, you are skipping the first post. To make this effective you would actually have to +1 to current post index THEN get the modulus, otherwise it will still skip the first post:

( $wp_query->current_post + 1 ) % 2

Hopefully that works!