Is there a chance the Video Mode (timeline resolution) is in 1920x1080? If the sources are 1280x720, they could be getting upscaled to 1080p, which could explain the blurriness and larger file size.
There are commercially available programs for limiting processes, like Process Lasso, but nothing directly in Shotcut.
Regardless, the real fix is to get better thermal management in the computer. Even if Shotcut was constrained to 80%, some other process like anti-virus or help-us-all Windows Cortana will be banging around in the background filling up the other 20% and your computer will crack anyway. A computer without adequate cooling will always be on dangerous territory.