Yup, the bosses ended up being "a bit" overtuned. The whole game kinda is I think. The spider boss specifically isn't really supposed to be taken on if you just straight come to it. I even added that warning note there right before it. But of course gamer brains don't take such warnings as true. You don't really need to beat the bosses or even quite a lot of the encounters to "finish" the game. And the bosses are indeed meant as an extra late game challenges when you have a lot of the upgrades.