No, if either or both the switches are 'on' the result will be the same. Activating the switch and the relay at the same time is just like having one of the switches on
if he does with parallel shouldnt he worry about sending a down command and then manually pushing the up switch causing a blown fuse at least.
just something to think about even if its rare to happen.
After taking a second look at my design, I realize that you could use 2 relays per window. In that case, you should hook the relays up directly to the window motor. For this setup, you would have the 30 terminal of each relay go to the window motor, and the 87 and 87a terminals going to 12V and gnd, respectively. This would not cause any problems with the switch in terms of the relays and the switch being on at the same time. I would not recommend hooking up to the switch anyways, since especially in newer cars, the voltage of the switch is essentially unknown unless you use a multimeter. Now that I think about it, there could be problems with this setup if both the switch and the relays are used. Hmm... I guess you could try getting diodes in there somewhere to make sure there are no blown fuses, but then again this problem would be solved with the 3 relays. Of course, I'm no electrical engineer, I'm just a hobbyist, so I would encourage you to get a second opinion. The diagram I listed earlier I just sort of came up with, which is how much of the electronics in my car goes.