Couple of quick notes when drawing.
Don't turn on "Ignore Top (2nd) Floor" in roofs dbx initially. That took me the longest to figure out. I'll show you later what it tells you.
Using the Garage as 0" and the main house as +1'4" causes Chief to build successive floors based on 0", not +1'4"
Why did you draw the foundation under left side of the main house and let Chief build the foundations under the right side of the house?
That's a rhetorical question. Isometrics show you built only the first floor roofs over the garage. I turned auto roofs on (next image)
Tried to clean it up and this ridge circled red kept popping up. The more work I did with the second floor, the more ridges and valleys started popping up.
It took me a minute to comprehend the 16" floor reversal was the culprit. Chief was drawing all my second floor rooms above 0' - I didn't want to continue this way so I,
Deleted your basement walls.
Selected all 1st level rooms that didn't have a floor on the left side of the house and checked "Floor Under This Room" in Structure DBX. Made the floor 0" here.
Selected the remaining rooms middle and right side of main house, made floor 0" here. "Floor Under This Room" was already checked.
Selected front porch made floor -4" here. (you originally had it 1' instead of 1'4")
Selected garage, checked "Floor Under This Room" and made floor -1'4" here.
This now looked identical to what you originally drew, with 0" the main floor and the garage -16". And then I turned Auto Roofs on.
Much cleaner. Then I rotated it and found your front porch and bedroom roofs are overriding the main gable. Examining the floor plan I found nothing matches up along your front walls to make a clean gable truss running straight through the home.....
So I extended the right front "closet" wall temporarily through the entire home. I changed it to blue so that you can see it.
I broke the left gable end wall at the blue wall intersection and changed the upper half to red. I also changed the right gable wall to red and then opened both walls and changed the roof to gables. Then I selected the front half of porch and bedrooms circled in red opened both rooms and changed them to roof group 1 (R-1). Also I selected the right wall of bedroom and made it a gable (forgot to highlight this - and the file I attached has all walls I turned to gable in red now.)
I also did the same thing to the garage bumpout walls (making them gable) and told Chief the back bumpout wall was a 6/12 pitch.
Then I made the blue walls invisible (but it still divides the rooms in two for now).
Much closer with Auto Roofs still turned on. But it doesn't quite match your original drawing.
Now, because you said the rear of your house has some vaults, I drew some second floor walls and this is where I discovered I had to turn off "Ignore Top (2nd) Floor" in roofs dbx because this wasn't permitting me to see how the 2nd floor at standard wall height interacts with the auto roof. I used the blue wall as the front of the 2nd floor room and extended it from the right bedroom to the left bathroom exterior walls. Made both endwalls gables, and the ceiling height 3'1-1/8" to match my original information (in hindsight 4'1-1/8" might work better to match over the garage... I then broke the front wall over the blue wall 10' left/right of the front door using temporary walls, made this broken section a gable, then copied your dining windows to this floor centered above the door. I had to raise them 2' to get them where you see now.
.Notice your second floor is sticking out of the roof over the garage, so you can see where it is. Now I'm going to play with your room over the garage. Most attic rooms inside room trusses will slope from 4' at the side walls to the allowable ceiling height. You can go lower, but I usually wait until I have room truss data to do this. At stairwell width, the a second floor flat ceiling has to drop from 8' to 4'10 1/8" before those extra rooflines disappears.
The stairwell is off center of the gable. Changing the room to no ceiling initially revealed an extra 1'7" to play with, And I dog-eared the doorway one foot at a full 80" high opening because the roof would impact it.. I also determined the room can also be 8'6 wide at 4'10" flat ceiling height.
Then I realized the program was drawing all roofs 1'4" above the ceiling plane of the 2nd floor.(SMH - this was probably my own fault when adjusting the foundation earlier) The right picture is after I corrected all your roofs. This forced a 2' dogear on the entrance to the attic. You could explore lowering the garage ceiling 1', but that means it gets closer to the laundry door (whose height doesn't change.) I can explore that later if necessary.
Changing the ceiling height to 4' room truss height, (4'1-1/8") also allowed the room to increase to 10'4" inside the room trusses (safely) Your truss guy will determine the actual width permissible. You may be able to lessen the dog-ear once you have truss data given the rigid foam insulation. I'd wait and see.
I then extended the front of this room to the outside garage gable wall, copied your dormer windows, making them 6'8 from the truss room floor and only 5' tall. I put red dots where you can see the 4'1-1/8" flat ceiling intersecting the windows. In glass house view you can see the room inside the trusses.
I renamed the 2nd floor stair opening room to open below. Broke my new wall over the blue wall to either side of the stair well and extended it back to the beginning of stairs. Added some room names and a text box that automatically calculates ceiling heights. Open Below is measured from the first floor.
Lastly, Why are your stairs 11" treads (nosing to nosing) which creates a 12" tread and 6-7/16" rises? Those are commercial dimensions. In residential we typically use 9" nosing to nosing, which results in a 10" tread, and less than 8-1/4" on the rise. typically 7 to 7 1/2 works well. This allow you to have only 14 treads to reach the next floor. The stair landing is then inside the laundry closet. Giving you more head room underneath for storage. I left your framing intact for you to delete.
All this with auto roofs still turned on. I made the blue wall visible again and saved the entire file as 3 and attached it.
Before you turn off Auto Roofs, delete all the blue walls - don't for get the one under the stairs. You'll find Chief is still building things automatically properly now.
If you turn off ceilings over the attic, you'll almost have the same room view that "Ignore Top (2nd) Floor" gives you. But now you know why the room can only be so large.
Now turn off Auto Roof. In attic room, change ceiling height from 4'1-1/8" to default 8'1-1/8". You can do this in 3d view while viewing the room. It changes to the same view you'd have with "Ignore Top (2nd) Floor" checked, but again now you know why it is designed the way it is.
Lastly, it looks like Chief builds soffits at the upper ceiling height and facia at the roof height, I think your 6" roof surface is causing this. Rotate your model and you will find a 6" gap between the siding and gable ends facia. Maybe you need to move the OSB/FOAM/OSB to the structure layer (like it is for floors) and let surfaces just be shingles & underlayment. I'll save this for later.