When hinges are fitted to a door you fit them say 5" from the top and 7" from the bottom so they appear evenly spaced from eye position. Maybe the same applies to ledges.
Might not apply to this old door of mine which is about to be re-hung for the seventh time
Thiambal - I agree with Worms. I would do anything possible to avoid removing the ledges from the door. You could do a lot of damage that would look worse than having the ledges in odd places.
Personally I would look for a way to cut down the door and re-use it with the ledges as they are now - even if that meant adding one or two new ones to "balance it up" visually.
In the end there was no way to cut it down and not lose one of the ledges. I did struggle with myself about just adding a new ledge and them being un-even - but just couldn't cope with the idea of things not being even.
Anyway, got the central ledge off quite easily - did a little bit of damage to the old ledge which I replaced but the door panels themselved survived with very little damage.
Made two new ledges, finished by hand to the same profiles of the originals and clinched in place. I am particularly grateful for the advice on clinching - I experimented a bit with some scrap wood and then it worked very well - screws? - bah! clinching is the way forward.