'Rape' is a tough one in this game. In most cases, you have to ask or put yourself into the situations where it occurs.
To answer as best I can:
1. Yes. You can be a male or become a Sissy and be submissive the entire game, and some of the women will 'use' you at times, using various methods.
You can get the Magic Dildo/Strap-on for Ava and she becomes a Futa (really) and Sasha is already a Trans, and they can both take advantage of you. You can also turn off the transformations, so that is a non-issue.
2. As I said, Rape is tough one here. Perhaps in the Dom John route you can get close. All other situations you more or less go there and expect something to happen...
3. I would read the Wiki in the OP especially for the John content, as well as view the Guide for Ava - it will show you how to dose Ava to get the scenes you want. Ms Dee can be aggressive also, also read the Wiki for her. And Penny later on can Dom on you!
Yes you can play as a Submissive male all the way through, or as a Sissy, and get taken advantage of by most of the females in the game. May take some time and several doses to get there, but it can be done (ie. use the Cheats to get there faster!)!
Enjoy!!!