There are two ways of dealing with orange peel. Prevention and sanding. If the painter is really skilled, he can shoot the paint and there will be little to no orange peel. If there is orange peel because the painter isn't that great, then the orange peel must be sanded out. Sanding means increased labor cost and that really drives the price up. Most shops view a certain amount of orange peel as acceptable and normal, as in how most factory paint is. I don't know what you mean by a certain way of applying the clear unless you mean to have them sand all of the orange peel out of the existing clear and then shooting more clear on top to have enough paint thickness for the long term. This is a necessity IMO, if you are going to be sanding the orange peel out of factory paint, because factory paint is so thin to begin with. Hey, it's already at the shop, so that is the time. However, It is going to cost probably 4-5 times as much to fix the orange peel on the whole car as it is to get a nice repaint of the damaged panel to either match the orange peel ness of the rest of the car, or to make that panel orange peel free.
Now, you COULD simply have them paint the car with the paint thick enough for YOU to sand and buff it yourself if you are up to it. They could either just paint it or paint it and give it a light buff to bring up the shine, and then you can sand and buff it out later. That would save you money I think. It will be a lot of work for you, but if you really want the car perfect, it might well be beyond your means to pay someone else to do a job that is as good as you want it when you could do it yourself. You can't paint, but you can sand and buff.
If they do paint the whole car from scratch, including the color coat, you have EVERYTHING to look out for. The more they do, the more flaws they can leave. Dealing with most body shops is tough. If you are a perfectionist, it can be extremely frustrating. I know, because I've been there. Oh, the anguish...
If you have the color coat redone, finding a great paint shop is all the more important. You need to see a few examples of their work, and don't assume that your car will turn out exceptionally well, just because you ask them to make it nice.
If it's just the clear that is redone, then just about any defect they leave can be sanded out by you.
It's a tough decision to make. If you want the color redone and you want perfection, you can't afford it. THAT would be a $30,000 paint job. Show car paint jobs are often $40,000. It's all the labor, and a lot of that is sanding between coats.
If you want to make the clear thicker so you can get rid of the orange peel, that would be an affordable option, though certainly more expensive than just repainting that one panel. Arguably, you could just have that one panel redone really nice, and then have the clear thickened later, but obviously, if you eventually want all of the metallic to match perfect, you must do the whole car at once, which brings us back to the pain of getting a phenomenal paint job at a price you can afford.
If I were you, I would probably have the one panel done and maybe put more clear on, and don't redo the entire car, because you will spend a lot more money doing the whole car, and it probably won't be perfect anyway.