Symptom: setting windowresolution in dosbox.conf has no effect when running programs in truecolor mode. instead, the window is resized to the program's native resolution.
Analysis: In src/gui/render.cpp, the GFX_RGBONLY flag is set in the gfx flags for truecolor modes. In src/gui/sdlmain.cpp, both GFX_GetBestMode and GFX_SetupSurfaceScaled check that flag for the 'opengl' output, and refuse to use it when the flag is set. Removing these two checks makes the problem disappear. (They appear to be a copy of checks for the 'overlay' output, which I believe works in YUV colorspace.)
Additional information: I'm using dosbox in windowed mode under Linux