Can't say for sure how Balatro did it, but typically you do one shared core and any platforms basically use that core in their own suitable way. Considering it's lua, would feel very natural and be relatively simple for Balatro to do it this way too. Not much to keep in sync, just ensuring the core remains reusable in the ways the platforms need it.
The Android and Xbox PC versions look more like forks for a shared codebase. Most of the platform-specific code is abstracted to a bridge, but even the bridges aren't consistent across the codebases. (Android's save system uses different methods than Xbox 's.)