I was looking over a Universal Wizard that I had rolled for a Pathfinder campaign that never lasted more than 3 sessions, and came across the Special Ability Hand of the Apprentice. Making a ranged attack off of my INT stat was really useful, but I never took full advantage of Instant Weapon, which gave me literally any weapon AND immediate proficiency with it. As such, I have two questions about how HoA works with special weapons.
Hand of the Apprentice is pretty specific. It doesn't make any allowances for weapons that are long or suspended from a chain, it's one ranged attack with a melee weapon against a target within 30 feet, treated as a thrown attack but aimed with Intelligence.
The answer to both your sub-questions is no, unfortunately. Unless you're using a weapon I'm not familiar with that has a quality that actually says "When this weapon is thrown through a creature's square in order to hit a creature behind, this weapon also has a chance to hit the creature whose square it was thrown through, as if X..." then throwing a weapon through someone's square just gives the end target soft cover against the attack, it doesn't give extra attacks.
Also, I hate to be a complete downer, but note that instant weapon doesn't combine well with Hand of the Apprentice. Instant weapon specifies "If the weapon leaves your hand at any time, the spell ends at the beginning of your next turn." It's missing the all-important clause "...unless the weapon has returned to your hand." so if you fling the weapon once with Hand of the Apprentice it will vanish at the start of your next turn.