GUI stands for Graphical User Interface, so yes pretty much everything you see on screen and that lets you interact with the sim, not just the TDC and periscope screens.
As fitzcarraldo mentioned, the interiors mod may have some side effect on parts of the GUI, so that you need to apply a fix on top of it. That fix needs to be activated after you apply the FM interiors mod. Personally I don't use that mod, but I would venture to say the fix files can be found in the downloads section. If not, I'm sure someone else more familiar with this mod will be helping shortly
As to what GUI to use, it's really a matter of taste and the kind of realism, look & feel, etc. you want for your sim experience. I have been using MaGUI Final for a year now and love it. I used the OLC GUI before it, and that was really nice as well. Both can be applied on top of GWX3; by "both", i mean they both work, but you cannot have them both running, it's one or the other.