It seems that the user.cfg is not supported, or it doesn’t work for me. Is there a workaround instead of adding all commands through ~?
Maybe a mod that adds user.cfg is needed 
Edit: So, the user.cfg is already loading but most commands are not supported. Here are the supported commands:
RenderDevice.Dx11Enable
RenderDevice.VSyncEnable
RenderDevice.TripleBufferingEnable
RenderDevice.ForceRenderAheadLimit
RenderDevice.StereoConvergenceScale
RenderDevice.StereoSeparationScale
RenderDevice.StereoSoldierZoomConvergenceScale
GameTime.MaxVariableFps
UI.DrawEnable
Render.DrawFps
Render.DrawFpsMethod
Render.DrawScreenInfo
Render.PerfOverlayEnable
Render.PerfOverlayVisible
Screenshot.Render
Screenshot.Format
vu.DrawFirstPersonModel
WorldRender.TransparencyShadowmapsEnable
WorldRender.MotionBlurEnable
WorldRender.MotionBlurScale
WorldRender.MotionBlurMax
WorldRender.MotionBlurNoiseScale
WorldRender.MotionBlurQuality
WorldRender.MotionBlurMaxSampleCount
WorldRender.MotionBlurFrameAverageCount
WorldRender.SpotLightShadowmapEnable
WorldRender.SpotLightShadowmapResolution
WorldRender.DxDeferredCsPathEnable
WorldRender.FxaaEnable
PostProcess.DynamicAOEnable
PostProcess.DynamicAOMethod