MOT stations normally adjust the headlight aim in my experience. As Steve says, it probably helps their stats not to on a car that's failed anyway. You will probably find they'll adjust if necessary on a re-test.
The sill failures are just metal moth starting to bite. If you have a sunroof, these drain into the sills on Gen 5's - built in obsolesance. It is possible to re-route or extend the drain pipes to drain under the car instead.
The inner sill is a pain to get to on most cars, better if you have a ramp. It's mormally only a small gap to suspension arms / mounts. Normally, outer sill corroded in same area so i tend to cut away outer and work from the other side.
A cheap fix is to weld a patch over each hole - your lowest quote will probably do just this. It will buy a year or 2 until the rust spreads further & breaks through again further along.
ideally, it needs all the rust cut out and new metal butt welding in (replacement metal cut to exact fit in hole). There is an internal structure within the sills which will also be rotted. This should also be repaired by cutting out rust & welding new, although it's not necessary for this part to look so good.
e.g. - corrosion caused by badly fitted side skirts with non-sealed fixing holes allowing rainwater ingress.
MOT fail
Under the skirt:
Removing the rusty areas:
Too much rust to remove all, so cutting away heavily corroded areas leaving fairly solid but surface corrosion - surface corrosion to be treated to slow rate of demise.
New metal welded in, welds ground flat, original skirt holes welded up.
Finished job
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