JacobB

Chief will automatically mull windows and doors when they have the same bottom elevation, the interior trim overlaps, and neither has an arched or shaped bottom.
 
You have a few options for preventing the automatic mull.
Remove the interior trim and use a molding polyline. Note: this takes the most work, but will give the best result. Offset the bottom of one of them a little: 0.000001" should do the trick. Slope the bottom of one of them a little: 0.000001" should do the trick. Note: this will prevent a sill.
 
Note: the fact that exterior trim overlaps are not considered when automatically mulling windows and doors is a bug.
AutomaticMull.plan

Have you tried adjusting this setting on the door (Jamb panel) instead of on the window? This setting was added to doors specifically to handle doors sized by the jamb/frame. Originally, windows didn't have this setting, but during beta testing users wanted it for windows as well.
 

For best results, you'll need to do some trigonometry to get the angles and edges to line up. The equations you'll need is: w = h * tan(theta). In your calculations you'll also need to account for the minimum side height of 1/4".
 
Note: the window width control will round values to the nearest 1/16", but the shape controls won't. You can best see this by changing the number style.
 

 
Without a plan, I won't be able to say why the wall layers have gaps.
 
You can, but I wouldn't recommend it. I could go into details, but the simple explanation is there are sections of code that don't work well when this happens (see the image below). If you really want to do it, set the window height 1/4" taller than you want it, set the shape control to the minimum of 1/4". Then use the object painter to set the height you want outside of the dialog. There are a lot of dialog restrictions that can be circumvented this way, but opening the dialog for that object and other updates can often undo it, and the dialog restrictions are generally for a good reason, even if it is just to prevent errors within a program. If you want some of these restrictions to be removed, fell free to put them on the suggestions forum.

9.2DegAngledWindow.plan

There are probably better solutions, but here's two that might work.
 
I probably wouldn't suggest using the wall niche route since it doesn't work well with the flooring and room molding, but it is an option. In either case, it will probably be finicky getting the shelving and cabinets positioned.
 

ArchedBuiltIn.plan

Hinged opening indicators point to the hinge or handle side based on the X13 plan setting @joey_martin mentioned. Schedules combine all rows that are identical, excluding the 3D Exterior Elevation, 3D Interior Elevation, and 3D Perspective columns. The image displayed in those columns is an image of one of the objects in the row, even if those objects do not all look the same. Doors have a hinge side (left or right) and a swing side (in or out). The size column displays the hinge side, but there isn't a column that automatically displays the swing side. You can add the swing side information to the door label or object information and include that in the schedule to distinguish between the different hinged doors.
 
You can look at the attached X12 plan that demonstrates this behavior with three different schedules generated from the same doors. Note that the size column also displays the hinge side and exterior/interior, not hinge side and swing side. Additionally, the hinge side defaults to right but the swing side is determined by which side of the wall you click on when placing the door. There is also a drag behavior that can set the hinge side to left.
OpeningIndicatorsAndSchedules.plan