"Can anyone tell me why the window insists on sitting so far into the wall as it is?"
Try the wall types in the parameters of the window itself.
I had a problem like yours and that fixed it.
Once you have picked right wall type for your complex profile wall there also might be one other setting, but can't remember right now.
Yes I have tried the other floor plan settings for the windows. Even if I can change it to look al ittle better in plan it still shows weird in section.
I have also tried the different wall type settings.