Guess the thread is a bit difficulty to follow and it all may look a bit confusing. But what I'm trying to do is to merge a Civ-type game with XCOM. In a fantasy setting. In the current state I have finished the battlescape (on-site) engine, and the geoscape (the world) engine, complete with all mechanics. Now I'm doing unit balancing, trying to give each of the many units some unique role. After it gets done, I will do a campaign encompassing several random generated world maps, each with different goals.
Compared to XCOM, battles are expected to be completed faster, and there is no save in the battle. The only opportunity to save would be on the world map. But I will try to prevent save scumming. Still I guess people could save-scum anyway, running in the emulator. But at least I could use the PRNG to prevent reloading to achieve different result. I.e. all sites are pre-determined on the world generation, so there will be no way to reload the game until it spawns the type of monsters which can be easily defeated by the player's current army. Same with AI, which uses pre-seeded RNG, so reloading wont affect AI's behavior. IIRC, Heroes of Might & Magic IV determined when player reloaded the game to save scum some chests with random content and locked-up the PRGN, although that could have been a glitch. But I believe the error was determining the chest content on the pickup stages, instead of at its generation time.
BTW, there was a somewhat successful merge of Civ and Warhammer as part of the Total War franchise. In fact, they even remade the original Warhammer Dark Omen campaign in the Total War engine. Earlier there was even a mix between Doom and Civilization - in the Sierra's Birthright game, which had Warhammer style army battles (dumbed down of course), but also site exploration part, looking like Doom and using a rather complex raycasting (?) engine for it.