Even though this guide is specifically for Muck, most of it applies to any Unity game.
Muck is compiled using Mono, which is cross-platform. I did notice that the hashes of the assemblies for the Linux version are not the same as the Windows version, but my mods seemed to work regardless.
Because assemblies are cross-platform, if your mod only applies code patches with no additional assets, you don't need to do anything about the AssetBundles. However, if your mod reads or writes any files to the disk, make sure not to hardcode backslashes! To work with the filesystem, use .NET's Path
helpers, they will make sure you write to the desired location!
BAD: