Unity lets you use either IL2cPP (AOT) or Mono (JIT). Either way it will use Boehm GC which is a lot worse than the .NET GC. If your game servers weren't using Unity then they are using a better GC.
Yeah, we rolled our own server framework in .NET mainly because we were doing MMOs and there were no off-the-shelf frameworks (including Unity's) explicitly designed for that. In fact, I believe this is still mostly true today.
