Everyone has their own way of handling oddities during installation. I got used to a method that seems fairly easy and whatever works is what counts.
If I make a cabinet with a face frame and it will be captive by either walls or other cabinets, I work out the details in my field measurements. Since the installation site is away from the shop, being able to fit and install on the job is critical.
I would take template material with me if necessary and determine what is out of plumb, or out of square. An alcove can be out of parallel, and a wall can be out of plumb, or have a bow or concave. Where areas are to be scribed, the cabinet is made narrow...to fit. The face frame will protrude from the end or ends, along with the floor of the cabinet. IOW, the front leading wall edge and bottom edge is able to be scribed (for an upper/wall cabinet).
My field measurements will include in determining what I have to work with. Using a cardboard template can produce what will have to happen to get a good fit. This same principle is used on doing woodwork or cabinetwork on boats and yachts, where there aren't any flat, straight, or square areas to work with.
I don't add stiles or face frames on the job. The cabinet gets fabricated to fit and/or scribed to fit. This pertains to custom work. For production cabinets, they are made in 3" incerments for width, and filler pieces are available to take up the gaps. Trim mouldings either flat, coved, or quarter round are used for final trim.