[*] 1. You can, using an undocumented command, /setlayer.
/setlayer <N> <windowname>
N is number between 0 and 255, with 255 being completely transparent, 0 being completely opaque
e.g.
//window -do @@1 10 50 200 80 | window -do @@2 220 50 200 80 | setlayer 220 @@1 | setlayer 110 @@2