I'm late on this, but there's something else you can try if you're still interested in messing with the "fullscreen but still windowed" thing.
I was running the game and getting ridiculous framerates, but it was causing some irritating coil whine. So I tried to limit framerates and it didn't work. Most of that is irrelevant to what I discovered, though.
Windows does voodoo in the background to "help" full screen games benefit from its built-in scheduling and other bells and whistles that generally make it easier to Alt+Tab in and out of the application and make all the programs you're running play nicely together.
If you go into your game directory and right click on the il2fb.exe, select "properties", and then go to the "compatibility" tab (just next to "general"), in the second "box" down on that tab, there are several options.
Check the box that says "Disable fullscreen optimizations". Apply and Okay.
Now the game will run in true fullscreen mode. The effect for me was that the GPU now caps at 240hz, which is the refresh rate of my monitor, and Freesync can just do its thing. And I don't have to listen to the squealing while the GPU rips out 1,000 frames that I don't need.
If I understand the Windows tech correctly, the fullscreen optimizations essentially "trick" the program into thinking it's running in full screen so that it can behave that way in the running environment, but Windows is actually running a windowed full screen so that it can keep everything else running on your system more easily and smoothly accessible. Disabling the Windows fullscreen optimizations removes that extra step. I've found that the graphics settings recommended for the conf.ini are a lot less prone to doing weird, unintended things with the optimizations disabled and the game running in a true fullscreen mode.