Sills tend to rot from the inside out as you have said, so if they're rotten on the outside, chances are they are worse inside. Rear suspension mounts are also a problem area and a potential mot failure. Don't take a chance on buying one without looking inside the door vents, surface rust is almost inevitable, anything worse, walk away unless the car is really cheap and you're prepared to pay big bucks for the repairs. Also check wheel arch areas particularly the bottoms of the front wings which can be expensive to replace if they are rotten. Get down and have a good look underneath at the floor pan and chassis, make sure it has not been damaged by being jacked in the wrong place. Take the car for a test drive and check for blue smoke on accelertion and when you lift off, the former indicates ring or bore wear, the latter valve stem oil seals or valve guide wear, check oil pressure is healthy, 4-5 bar at 4000rpm and at least 2 at hot tickover. Also listen for a whining gearbox.
When you go to look at a car, have a notebook of areas to check, its easy to forget areas if you are not methodical.