Perhaps I'm looking at things a bit differently, but it doesn't or shouldn't take a full restoration shop to do "straight" body work. Nor should it take a restoration shop to get a good quality paint job using OEM-spec or better materials. Panel gap alignments will be governed by what the particular vehicle had to start with. Certainly, the restoration shop would be expected to take more "care" in the bodywork being as good as it can be, using several primer/sand operations before the color goes on. Which would probably yield a "better than new" appearance, in many cases.
As they say in the article, it depends on what level of restoration you want, and you should sort this out with the shop before selecting a shop, getting an estimate and beginning the work. I wish I'd seen an article like this when I was looking for a restoration shop, but fortunately I am happy with how things turned out for me.
A proper restoration shop will want all of the chrome trim, door handles, etc. removed and likely want to take the car down to steel before repainting. They don't want their work to be applied over old bodywork where they don't know how well it was done. A collision shop would be more likely to do a "scuff and shoot" over the existing paint, and will tape over trim, door handles, etc. instead of removing them, unless you remove them first or ask them to do that as part of the job.
If you're replacing body panels, that will affect the panel gaps. For example, for my Windsor resto, the shop and I agreed that it would be more cost-effective for me to find and ship better doors than repair the rust on the ones I had (BTW, thank you again
@azblackhemi). When my body guy "Painter Paul" bolted them onto my car, he discovered that the drivers door lined-up well but the passenger door was too far forward for some unknown reason. He had to shim the hinges to move it rearward to fix the panel gaps. Additionally, the entire front clip on my car was coming from a parts car, so all the panel alignment had to be redone from scratch.
If the body is being taken down to steel, you should get the metal sealed with epoxy primer as the first layer. Restoration shops will do that, but collision shops don't normally apply epoxy primer. I needed to replace the trunk floorpan in my '66 Windsor. I cut one out of a parts car which I was going to weld in myself. I took it to a shop to get sandblasted, then to a local collision shop that I dealt with previously for work on my daily drivers and asked them to epoxy it for me. They said they only use water-based paints now. They didn't want to use epoxy primer in their equipment because it would be a special order, and would require extra cleaning to ensure no contamination with incompatible solvents, etc. So I let them spray it with the primer/sealer coating that they normally use instead.
I'm sure a restoration shop will take more effort where rust repair is necessary. In my experience, collision shops today are used to pulling out dents or buying new/reproduction panels or getting used ones from the scrapyard, not repairing rust damage on existing panels by fabricating patch panels. That is a time-consuming and skilled process to do well. For cars like ours where new panels are not available and good used ones are no longer available in the wreckers in many areas, a collision shop is probably going to spend less time fabricating and more time applying bondo.
My '66 Windsor was previously restored in the 1980s, probably at a collision shop. Some of the trim was just taped-over. My outline moldings were removed but the clips were left in and painted-over. For rust repair, new metal was pop-riveted over rusted-out sections and then skimmed over with bondo in some areas.
It was obvious where bodywork had been done in several places, because not enough time had been spent block sanding nor feathering the bodywork into the existing paint.
A collision shop would likely use air-powered orbital and straight-line sanders which are maybe 2 feet long. In contrast, Painter Paul block-sanded my car by hand. He made custom sanding blocks for my car which were 4 feet long, so that the bodywork would come out perfectly straight during block sanding. The results speak for themselves: