I already explained to you how you are generating clips at full range without signaling it. Of course, that is going to lead to incorrect results as I already demonstrated in the other thread on intermediate files. Until you fix that, your tests are invalid, and you need to stop making claims without evidence. Meanwhile, I provided some counter evidence to this claim in that thread. Of course, it is not perfect, but it is much better than what you were reporting while using a faulty process.
whether Shotcut addresses individual pixels
It depends on what you mean by “Shotcut”. Strictly speaking, no; except in preview - when not using GPU Effects - it receives YUV from MLT and uses an OpenGL fragment shader to render in RGB. If you are referring to the whole build with FFmpeg and MLT libraries included, then, of course.