You can definitely remove notes from a scale by using the scale editor. It is a slower process than using something like the intelligel, but the power of the editor is worth it.
Here is the “incomplete” manual – https://tubbutec.de/files/uTune-user_manual-v.1.00.pdf
Section 4.3 discusses using the scale editor, which allows you to take the existing scale, and modify the distances between notes, but also lets you disable the the specific intervals you want to “turn off” (like, limiting a 12-Tet scale to just a pentatonic, or something like that)
You can definitely both use both channels of the module with two different inputs (meaning, you could use two different CV inputs, or even 1 midi, and 1 CV input, or anything similar), however, in the current version you are limited to one scale for both channels (as far as I understand it). I read a rumor somewhere that we will have separate scales for different channels in the future though…