Beyond All Reason is a SpringTA fork (hack? build?) like Zero-K? So the underlying engine isn't Lua, but higher level scripting is. I'm pretty sure this is fairly common, or was once.

Other games with Lua scripting: Roblox, Baldur's Gate, Civilization VI, Crysis, Factorio, World of Warcraft, Far Cry, Leadwerks, Friday Night Funkin', Foldit, Garry's Mod, Aquaria, Balanced Annihilation, Bitfighter, Bos Wars, Cataclysm, CivCity: Rome, Civilization: Beyond Earth, Company of Heroes, Cortex Command, Counter-Strike 2D, Crimson Steam Pirates, Dota 2, Dungeon Crawl: Stone Soup, Dungeons, Dungeons II, Dungeons III, Elven Legacy, Empire: Total War, Escape from Monkey Island, Eufloria, Exodus from the Earth, Angry Birds.

Here they are:

https://github.com/beyond-all-reason/Beyond-All-Reason

https://github.com/ZeroK-RTS/Zero-K

Also Supreme Commander