Okay, I see where the confusion is.
Your point #5 is not what I intended for the rules. The intent is that you only remove dice if two or more dice show the same top value. You don't just remove all dice that aren't the top value – you only do it if there's a "tie". The rule says:
First, if two or more dice show the “top value”, remove all dice that do not show that value.
In other words, if there is a tie for the highest value (across all four dice), then you eliminate anything that wasn't part of that tie. If there was only one die with the highest value (which will fairly often be the case), you don't remove anything.
Sorry for the confusion! That rule as written might be a little too terse, making it easy to miss the nuance there, so I'm going to add some clarifying language to that section in the rules and release a new version soon that might help me convey the rule better for future players.
Thanks for taking the time to talk about this with me – if you got caught by my description of the rules, it's pretty likely others have, too, but never spoke up about it, so I appreciate it. This will help me clarify the rules not just for you but for other players as well!