Update on missing window and another concern!

We emailed both our SR and PM about our concern with what appeared to be a missing window in the master bedroom.  Our PM emailed us back and said that he would confirm all windows once the roof was finished.  Our SR called my husband today and said according to his records we did not choose that window as an option and only chose the side loft window as an option.. My husband explained that we didn't choose the side window in the master bedroom because we were told that there would be a double window on one side of where we would put our bed and another window on the opposite side.. well then he came back and said with the morning room as a chosen option that it's actually only a double window and then we would automatically get the window on the side..

Needless to say, during the pre-construction meeting it was noted,discussed, and signed that we would be getting (not buying) the side window so we never thought to confirm that..

Anyway, PM emailed us tonight and said that he put in an order for the window and that it will be in next week.  So now this is our next question/concern but I'm hesitant to email our PM about it (I don't want to seem like a pest)... but is this how they build morning rooms???  Take a look at the pictures and tell me if this looks normal.

Do you see what I am talking about?  Why does it look like that is going to be a door and not a 3rd window in the morning room??  I'm hoping they are just cutting more wood and putting it at the bottom and framing it for a window.. it just looks completely different and why would they do it that way?

Closer shot of it

This is supposed to be our double door.. it almost looks to high up to be that though..? 

View of the morning room from the outside...

So weird!!!  Anyone have any advice?  Should we wait to see if its just their way of building or should we email PM right away?

Anyway, here are just a couple progress photos..  I didn't take too many because I was so distracted with the morning room.