1. Yes, you have to choose accepting Jeremy's abuse. Refusing automatically puts you on the Diane path, leading to different scenes, the most notable in the last update with anal sex on the plane or MFF threesome at the beach.
Furthermore at one point you have to choose between Robert and Jim for help getting the documents back, leading to different scenes and so far one extra scene if you choose Jim (MMF BJ scene at the bar)
2. Yes, you can miss the earlier Alfred scenes, you can miss the black dildo mirror scene and you can miss the hot-dog scene if the player isn't paying attention to the dialogues.
3. No idea
You could always compare with my Ren'py version which has a fully unlocked replay room letting you tweak the variables so you get to see every variation of every scene. Word of warning it does have almost every game scene in it, even the smaller ones like the phone calls in the office.