To preface, this may be a function of the OpenGL renderer vs. Software because ZDoom seems to handle all the below behaviors extremely smoothly. Still, it seems incorrect and hopefully it can be fixed. Also note I do not recall experiencing any of these problems on Windows, but it has been a while since I played there and I may not remember.
First, any mode change causes the display to "grab" the underlying/previous graphics and hold them in the window for a moment before updating. Some screenshots in spoiler below, click for fullsize.[spoiler]
Scaling DOWN a windowed mode
...
Scaling UP a windowed mode

[/spoiler]
Now, that's annoying but not too big a deal, but the next problem is worse. Running in fullscreen in less than native resolution
does not scale to fit the display. Screenshot in spoiler. [spoiler]

[/spoiler]I've tested both ZDoom, Chocolate Doom, and
Amnesia: The Dark Descent in non-native resolutions and all work 100% properly (
supplementary screenshot). Additionally, switching to/from fullscreen also displays the same behavior noted above.[spoiler]
Switching out of fullscreen

[/spoiler]
Honestly this isn't the end of the world, but it's certainly annoying and makes me enjoy GZDoom on Linux slightly less. Hope it's maybe possible to fix somehow.