What? Maybe I don't understand the problem, but of course you can rotate elements in FreeCAD whichever way you want.
Select the object, set orientation in Placement / Axis / x,y,z
Select the object, set orientation in Placement / Axis / x,y,z
- Create a square via the CreateSquare[0] icon
- Put the lines as construction line
- Constrain the holes to the corners of the square.
- Add an angle constraint on one side of the square as you need.
It's easier than constraining your holes on a rectangle on which you have to replace the horizontal and vertical constrains afterwards. And you get to keep all those parametric variables that make changing something afterwards so easy.