Nice stuff. The magic supply chest I feel was definitely the right choice. You still got stuff to do, but it's not too much of a complete grind. I do feel that giving baths could also do with some refinement, as one of the "leftover repetitive tasks" - it's fine in the beginning, but towards the end of the current content, 2 favor are really not worth bothering anymore (so, okay, you can just not, but personally I'd rather see ways to improve favor-gain as the story continues for this bit).
Tendentially I agree with most of the things others have posted; I'd add that keeping the portal charged and keeping enough oil around is maybe a bit too easy now. Not that it was difficult before, but I feel like I'm swimming in resources (esp when Nyx joins, but even before then). The Totally-not-RISK game definitely needs some adjustments but apparently they are coming so I'm fine with that. I'm not expecting some super-complex minigame there.
In addition to all the other suggestions about it I'd personally like to see some sort of "we're getting attacked!" events; like randomly about once a week or so (player getting notified in the morning so you know to focus on the portal that day). Then a lot of your frontline fields get randomly hit (perhaps they are marked with swords or so?) and at the end of the day they randomly lose 1-5 crystals ... or something of that type. Either way, a more serious counter-attack mechanic so to speak.
Speaking about that minigame, would be nice if the Convert button showed the conversion rate. Real small detail, but would be nice.
And while I'm at small details, dunno if it's just random, but I'd find it helpful to keep items together in the inventory; esp. along the upgrade paths (iron -> silver -> gold -> platinum). At least for me some of them are (like the wood ones are all next to each other I think), but others aren't, so it can be a bit of a "search" to see how much you got overall of that path. But, again, real small inconvenience; not exactly super important.
Overall though even if nothing changes and the game just concludes the plot I honestly wouldn't have an issue with that. Yeah, it'd be a bit grindy in places but there's nothing there that I find too tedious; once you kinda figure out what's what you can progress pretty fast and ease and the characters definitely make it worth doing so.