Thanks for all the comments. Really useful to find out that other people have had similar problems.
As a result I decided to tackle the two 10p sized bubbles on the nearside sill. The corrosion had spread under the stone chip paint, and I ended up with a 7cm long hole in the bottom of the sill. Fortunately the damage was quite localised, and the rest of the sill appeared sound.
The hole was big enough for me to investigate inside. It seems that there is a design problem, with any moisture in the sill or in the C-post behind the rear door collecting in this area, with no obvious drain hole. The problem is made worse because I park on a slope, with the rear of the car lower than the front. It also appears that there is inadequate rustproofing in this area, with little if any wax inside this part of the sill. There is wax further towards the front of the car, and I think that when the car was manufactured the wax was injected through the hole sealed with a rubber plug below the front edge of the front door. So the wax may not have reached the rear of the sill.
(There is another rubber plug inside the rear wheel arch (hidden behind the rubber dirt shield) but this appears to give access to another box section, which is an inner upper sill rather than the lower outer sill.)
My local bodyshop welded up the sill and painted it for £200. They reported that the damage was very localised, and the rest of the sill was sound. My first spend on the car in 14 years apart from routine maintenance - amazing! I then rustproofed the area (see below).
So - here are my recommendations for IS200 owners.
1 - inspect the rear of the sills for signs of rust bubbling under the paint. Look about 10 cm in front of the rear wheel arch.
2 - if you find any bubbling, don't touch it until you have checked your anti-corrosion warranty. Mine had a 6-year warranty, but someone on this website said they thought they had a 12-year warranty. If you are covered, take it to your local Lexus dealer for inspection. If you do investigate it yourself you may invalidate any warranty.
3 - if you are not covered and you have more than minor bubbling, the sill may be corroded and need welding. It may still get through the MOT because the stone chip paint masks the extent of the corrosion. But the area is close to the rear jacking point.
4 - I would recommend ALL IS200 owners rustproof this area, either after welding or for prevention. I drilled two holes in the bottom of the sill about 50cm apart (can be done with the car jacked up and supported), and also used the hole with a rubber plug below the front of the sill. Drill the holes just outside the flange. No point in drilling the other side of the flange as well, because it is the same box section. I used Dynax rust treatment, because it comes in a 750ml jumbo aerosol with a 60cm probe to get into box sections. Dynax came out well in a survey a few years ago, and I have used it a lot on my classic car. The probe makes it much easier to apply than Waxoyl, and the fluid seems to be more effective.
While you are at it, lift the spare wheel cover in the boot, remove the rubber plugs in the bottom of the wells behind the rear wheels, and spray the area with Dynax.
It took me less than an hour to treat both sills, bot a bad investment to extend the life of an amazingly reliable car.