After playing again for a while...
One problem as mentioned earlier is that resources in this game are now of a limited quantity, which can make complications.
Maybe there can be a new scroll one can make to create new chunks (on the same square as another chunk) or overwrite an old chunk? An exploration scroll?
Am I using the term chunk correctly? An adjustment I would make to the surface missions is that in order to get a spell, you have to complete a series of missions. Right now, just doing one mission is very quick and trivial. If a series of missions were required, the spells could even be upgraded depending on how long the "quest" is (you could get a rare spell for completing a string of 6 missions or so; do 8 missions and beat a lieutenant-level boss to get a legendary spell [make these quite rare or craftable of course]). This would also solve the above note that the surface spells become worthless over time.
In terms of secret missions feeling "grindy", I don't agree very much. There's the excitement of exploring and battling your way to new areas, and the chance of getting a bonus-granting structure (like a lighthouse or a "?city fungus garden?"). I feel more roadblocks in this game are needed to add more substance to this game, maybe it will make exploration for "the grind" more fun as well.