If I accurately understand the recon-all script, then -noaseg sets UseAseg=0, but "autorecon2-noaseg" is a different flag, which only sets the following things.

    case "-autorecon2-cp":
    case "-autorecon2-noaseg":
    case "-autorecon2-wm":
      set DoNormalization2 = 1;
      set DoSegmentation   = 1;
      set DoFill           = 1;
      set DoTessellate     = 1;
      set DoSmooth1        = 1;
      set DoInflate1       = 1;
      set DoQSphere        = 1;
      set DoFix            = 1;
      set DoMaskBFS        = 1;
      set DoWhiteSurfs     = 1;
      set DoSmooth2        = 1;
      set DoInflate2       = 1;
      set DoSegStats       = 0;
      set DoCurvStats      = 1;
      breaksw

Best Regards,

Gabor