Why not let Aura enter Riverflow on day 1 even though everybody is sick? The sick townsfolk don't actually offer anything. And Jacob's house could just have a bit where he's dealing with his daughter's tantrum and asking Aura to leave. Enabling these would just give players the option for a theft I edge case with the apples.
Northern mine could just be filled with spiders but no teammates, which would bring it in line with doing winged pig thief without Charlotte or killing various bosses before they become objectives(first goblin shaman, first ogre commander, second low demon, phantom lord..).
Nephlune day 1 could be balanced by having the vendor start with fewer restocks and the door to Lilliana's house locked(she's not home, which also means you can't unlock the Mary disguise), so it mostly just allows players to use the collar to win duels, rushing wind slime as a substitute for new game+, or to grab early books. Slave trading isn't available until vice gets unlocked anyway.
Bridge bandits being a multi-stage battle effectively blocks off the south unless Aura goes for a pink run, which would stack additional rewards onto said pink run.
Belphegor is gated by needing to know open domain I and 100 mp to learn open domain II, mount Firestorm is gated by needing water skin II or excessive amounts of healing items.
Verdeaux might need some work, but the restocking vendor can start with less inventory, anything involving Roland and/or the princess can be gated behind the festival of greed, the cathedral is already gated behind Belphegor, and just about everything else is gated with gold.
I can't remember if sequence-breaking Sathanas and Arwin would actually make the dialogue confusing, but if you somehow manage to sneak far enough into Draknor fortress with a blessed energy potion+ just to get a curse trap barrier before saving Edwin, you probably know exactly what you're doing and should be allowed to dodge the willpower hit.
Locking off the more high-level areas just means Aura is less likely to accidentally end the day early and denies players opportunities to get ahead by being trying to be clever, both of which would actually be rather on-theme for this game.