I don't think 1mm is deep enough to worry, a base grind can take care of that. Anything deeper and I'd use ptex, and if it's a core shot then epoxy will go in before that.
Difference between black and clear? It's to suit your base color, but with clear being harder to "look good" because you will probably get some carbon in your repair, especially if it's your first time.
Consider the scratches, 'customizing' and not performance related, until they are across the base and become obvious gouges. FWIW, ptex candles are a temporary fix anyway, and when you need to repair them, welding will last much longer and possibly indefinitely.
Once again, you don't need perfect bases. Don't worry about most of the little nicks, gouges and scratches. Just keep waxing and skiing them. The wax is what makes them fast, not having perfect structure.
The only thing I'd check is if the scratch (gouge), went deep enough .... though not to the core ... pushed some of the base material upward where it is now above the base of the ski. You can feel this with your fingers or use a straight edge ..... if you can feel it above the rest of the base, you can lightly shave it off with the "flat" of a conventional razor blade .... that is to say ... just shave it flat to match the rest of the base.
Good point. Like edge burrs versus nicks, the little 'innies' are OK but take care of the 'outies'. Little imperfections will not ruin your glide (or your boards). Look at all the variables on any given slope at a given moment which are far greater than a minute nick or bump or undulation of your bases. Don't sweat the small stuff....but pay attention.