None of these computer programmes can teach airmanship, situational awareness, or lookout.
No they can't, nor are they in anyway designed to, but by enabling the student pilot to practice procedures and use of checklists they can be of benefit by freeing up mental capacity for threat and error management, situational awareness and lookout when flying for real.
Even the simplest flight simulator, if used imaginatively, can be of benefit in some way or another.
The only bad habit I have found is that students can become glued to the instruments rather than looking out when flying visually - in that sense I agree entirely.