BY DESIGN:
Neither CommandBuffer.ClearRenderTarget or GL.Clear clears more than the first color buffer. We currently don't support clearing all MRT targets, and would need to introduce a better overall interface to do that.

Your only current option is to bind and clear multiple times.
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Steps:
1. Open repro scene (repro project in comment)
2. Hit Play
3. Observe on game view

Expected Result: The screen is gray + cyan quadrant in the bottom left hand corner
All render textures specified in the RenderTargetIdentifier should have subsequent graphic commands ( SetViewport, ClearRenderTarget etc..) applied to them if the identifier is set using SetRenderTarget.

Actual Result: The screen is gray
Only the first render texture specified in the RenderTargetIdentifier is affected by the subsequent SetViewport graphic command.

Reproducible With: 2018.2.0a2, 2018.1.0b9, 2017.3.1p1, 2017.2.2f1, 2017.1.3p1