The intended gameplay loop of challenging bosses is unclear

This is only the case for the first boss. It is not an issue on other bosses since you have the city unlocked. Also, there is a hefty crafting mechanism which allows you to craft EVERYTHING you need. Gear, food, potions, usables, weapons, you name it. If you are smart about it, you stop throwing money at everything and use the money you farm to get self sufficient. In the end game money is not an issue anymore anyway.