One of the few things I would like to is try to astain what the cause of this is and the solution to this slight irritation of mine.As you can see in the photo there is a noticeble step where there is a mismatch. Well I say noticeable, but i think if you didn’t own it you would never notice! 
Thing is it runs the length of the mid section of the car. Front arch, Door, Rear Arch.
Option 1 would be to try and blend it somehow so the step can’t be noticed. But i have heard this may be some sort of rust protection? and might not be advisable.
Option 2 Is stick some Dark Grey GT or something style side stripes over the step.
Option 3 Ignore it(Easier than it sounds!)
I’m pretty sure thats the original stone chip protection and its supposed to be there . Its on my mk1 up to the body line, if my memory is right its on my brothers as well . If you don’t like it i’m sure it would be a body shop job to sand it smooth and then repaint both sides of your car .
Sometimes after sill repairs body shops will paint to this line as its eaisier to stop there than blend up the whole body which could look far worse if its doesn’t quite match.
In my opinion its supossed to have dimply stone chip down below so option 3 for me.
If you have deep pockets then you can paint it how you like .
Its pretty difficult to see from your photo just how much of a lip there is on your repaired sill in the photo, but as you can see on the photo below, Mk2s have a very definate line where the stone-chip ends and the smooth paint begins… On this car it looks like a very definate step existed before the repair was carried out well below the stone-chip line 
Finished job:
Dr. Eunos 
Thats fine then 
If it’s meant to be there it’s good for me, just seemed a bit heavy. Maybe on a Sill repair it’s been done. I’m assuming the sills have been done as there’s only the tinyist spot of rust on the arch, with a 12 year old car I’d be lucky if the originals have lasted!
Cheers Dr Eunos made me feel much happier. 1 Less job on my MX-5 To Do list.
Next job ahoy!!!