there is no negative feedback as long as it is constructive and made to aid the game to become better! :) So don't be afraid in posting anything you find that you think it can improve the quality of the game in any aspect!
The core rulebook, gives you an idea about how everything in the game works and explains anything you need to know in order to understand the game.
Then, comes the scenario. The scenario always, overrules anything if it wants to from the core rule-book.
For instance. If the core rule-book says "Raiders cannot be moved into or out of a starbase sector by any means". And in a scenario it says "you are allowed to built a starbase on the jump-gate sector".
That means, that if you built a a starbase, on the jump-gate in this specific scenario, then the raiders will never be able to enter the jump-gate sector.
Also to answer your "what happens if 2 bosses appear on the same hex".
I find it really intriguing and amazing on how you actually managed to do that, and i am really, really anxious to know how you accomplished that! But, no matter how awesome it sounds, you can't do it. A boss, can never be on the same sector as an other boss.