OK, to take the issues one at a time:
Disguise skill assumes you have a normal level of disguise equipment just like auto mechanic assumes you have a tool kit and spare parts. If you can't come up with a lab coat and some Groucho Marx glasses, you'd be at a penalty.
Yes, I'd allow use of a facial/body scan to program a latex mask/nanite kit. It makes sense that such kits would be compatible with major biometric software. As per RAW, the Rating of the disguise kit then equals the rating of the scanner device. Yes, that means that its often more effective to use Computer+Edit unless you have the time to specifically set up a high resolution scan. Vegas has basically ditched facial recognition software because it generates too many false positives. They found that trained people could do a better job. So this makes sense.
Most biometric scanners don't actually produce useful data for a disguise kit. Hand shape, breath, cellular, DNA, gait and finger/retina/tongue/whatever prints are not something a disguise kit can duplicate. So its really down to facial recognition or a full body ultrasound scan.