Let me do a bit more research and I’ll try to get back soon.
Edit:
I actually found the conversation you were involved in on github last week while searching, and SDL’s issue 11041, which was mentioned in the former. (I mention both because they may be helpful to someone else)
I see that Slouken basically says that the setup is worth some users hitting the delay, and that it’s partially an openGL optimization decision.
There is SDL_SyncWindow() which will attempt to pause the program until resize is completed, but I don’t think that helps delta-time games or online multiplayer.
Could you do me a favor and try hiding the window directly before calling the transitions to and from fullscreen?
SDL_HideWindow(window);
fullScreen = !fullScreen;
SDL_SetWindowFullscreen(window, fullScreen);
SDL_ShowWindow(window);