If you've got the same sight picture and the same shoulder alignment, the shot should go in the same place. I remember a tournament where I was the last in my group to shoot, and it was the only shot where a sitting position was required. Everybody else missed. I noticed that several people were facing the target from the seat, and I wondered why they were doing that. I sat down sideways, even though the seat wasn't facing that way, so I could get in alignment with the target. Once I came to full draw, everything looked and felt the same as a regular shot, and I hit the target.
That said, you want as much to feel normal as you can when you hunt, which is why you should practice shooting broadheads, sitting, or whatever else is going to be different before you hunt. Your mind has enough different to worry about just seeing a live animal without a whole lot else being different.