To be honest, at one point it certainly annoyed me. I got a game over because of despair, because of Mudo and Hama, even because I neglected healing the MC and the enemy got "1 more" on the next turn. I lost quite the progress every time, which really is frustrating when the Palaces' Safe Rooms aren't close. However, I really love how these failures had me to basically reorganize my entire strategy around the MC rather than the team. You're supposed to build your team around the MC. Joker can essentially equip numerous different attributes, buff spells and weaknesses/resistances that can change at the start of the battle and can even change the team's composition during the battle. As I see it, you're not supposed to die on enemies you know.
New enemies are the main problem with this mechanic, but I feel like the "Take your time" motto is apt in this case. Scouting for enemy weaknesses, while protecting the MC, seems essential. Trying to beat a Palace in 1 day means you have to face about 10 different new foes and I'm sure some of them will have an annoying trait that can potentially chain the MC to death. After knowing your enemies, which may take a couple of battles or more, it's extremely easy to trigger a Hold Up, which basically means you have a high chance to 1hko the entire enemy team.
Also, save all the time. I think it's preferable to do some back tracking in a section you cleared, facing beaten enemies again at worst, rather than trying to advance without knowing when you'll find the next safe room.