Can I connect both layers of a single SC6000/M to different channels of an analog mixer for scratching?

I recently acquired a Vestax PMC 06 ProA analog mixer and I was thinking of buying a turntable, but then I saw that the SC6000M has two line outputs (Layer A and B) and would fit the bill as a portable scratch setup, wherein Layer A would be connected to one channel for break beats/drum track and layer B for the scratch sample/scratch track.

Will this kind of setup be possible?

Yes but you can only scratch on one layer at a time, obvs.

Shame the Vestax does not have fader start option, then you could use it for the Layer A of the SC6000M (the REMOTE socket).

Yup. And switching btwn layers is one button press away. You can even change the lighting of the decks to your liking so you can visually differentiate between layers A & B.

While I am no scratch DJ, I have done this exact thing to practice, even with 4x SC6000Ms.