The food and mana are definitely a problem in the current build.
The problem as I see it is that the world generator was likely balanced for the original interpretation of the strategic game. The pyramids, for example; because of their rarity, generating mana from them required a constant influx of scrap to keep them going each time Demonaica destroyed one, and they were always a high priority rebuild because of that. Farms were kinda similar, though not quite as hard to deal with.... UNLESS you hadnt encountered enough of those Shallows areas; but you could always at least re-build the rare but useful "basic" farm tile.
The worldgen seems set up to make that work, and in the current version, this can lead to lack of resources not due to stratigic errors by the player, and not due to Demonaica's actions, but due entirely to the whims of the RNG. This means that food is hard to deal with, partciularly if you only have one Shallows biome area open to you currently, and it means that mana is nigh-impossible to obtain.... there's not much at all you can do there, and the moment you get one of those pyramids up, well.... chances are, it's not going to last very long.
My thoughts on this, is that with the changes to the way the actual gameplay works, some changes to the worldgen might be needed, and possibly even the introduction of more tile or building types to give more options for those important resources. The strategic part of the game is coming along nicely as it is right now, but this bit is the part that can currently lead to major frustration.
I'm interested to see what kinds of defensive options might be added here, though. That sounds like a good addition to all of this.