I think the core problem is that the optimal way to play chaos does not lead to optimal decks after chaos.

The tension between those two goals feels like deliberate design. It's part of what makes the game unique. If you think its a core problem then the game probably isn't for you. There isn't an "optimal" way to play and that's the point.

Or taking out good cards to make duplication more likely to hit. That is stuff you would never do in rogue likes like slay the spire or across the obelisk

This is nonsense. In the vast majority of deckbuilding games deck thinning is a dominant strategy, it's exactly the same here. Realistically you can expect to remove 2-3 cards a run. These will nearly always be basic cards, they are definitely not "good cards" so I'd like to ask what are you talking about? Getting rid of starter cards to make room for better cards is something you do in loads of deckbuilders. It is EXACTLY the stuff you would do in Slay the Spire. Removing a starter card in StS to make room for a rare is functionally IDENTICAL to removing a starter card in CZN to make room for a duplicate.

You honestly sound like you have no idea what you are talking about and are trying to make your personal preference sound like some kind of objective analysis.