The stub thing was what tipped me off! I’ve made this mistake before, sadly enough, where I’ve put an incorrect version of SQLitePCL.Raw in for whatever platform. I put the stubs in on the other platforms because they are not needed and cause more error messages on other platforms, but on the standalone version it should be there (it should call the native SetDllDirectory from kernel32.dll). That’s why the logic had no effect for you but worked for me (my DllDirectory was already cleared, but apparently yours is not and clearing it had no effect because of the mistaken stub). I ran this on my OS X machine without the proper #if guard and noticed the error message telling me that kernel32.dll could not be found, so I’m pretty sure it’s the right version now.
Also, about the duplicate symbols, beta 2 and newer no longer have an assembly called Couchbase.Lite.Unity. I was building it on top of .NET 3.5 Couchbase Lite before, but now it’s a first class project built right from the shared project, and so has just a Couchbase.Lite assembly like the other platforms.
That being said, I had already done some upgrade work on my OS X machine, but not pushed it. So the DLLs are newer now but not the newest. However if you attempt to replace them like you did, it should work this time. I’ll push up what I’ve got so you can have a look.