Unity supports both IL2CPP and Mono scripting backends for Windows builds. IL2CPP converts your C# code into C++ before compiling it, which can lead to performance improvements and increased security. Mono, on the other hand, uses Just-In-Time (JIT) compilation, which can result in faster build times during development. The choice between them depends on your project's needs. For final builds, IL2CPP is often recommended due to its performance benefits. However, be aware that IL2CPP may require additional configuration to handle code stripping appropriately.