As an insurance adjuster I have been to 1000's of body shops. From dealerships that are personally inspected by Roger Penske, audited by manufacturers, have laser welders, dedicated aluminum bays, and side loading paint booths to hole in the wall shops, some that haven't been updated since the 70's.
I don't recall ever going to a corporate or franchise shop that was messy. Sure, I've seen some disorganized tool carts in these places but generally they were organized and well run. At this scale there are regional managers and a chain of command up to the C-Suite that sets standards and maintains SOPs.
Then you have the high level mom and pop places, some that are working towards being bought out by a franchise. They might have 2 or 3 locations. These are usually on par with corporate shops as they have gotten there through hard work and organization. The office is clean and they are tough and knowledgeable estimate negotiators. Running a finely tuned shop as a smaller business is not easy but if you do it right you will attract insurance companies and will be able to obtain manufacturer certifications allowing you to compete with dealership shops. Afterall, a manufacturer won't certify you if your shop is messy and doesn't have top of the line equipment and a budget to afford manufacturer specific tooling.
The medium level mom and pop shops might have family working in the office or in back. They usually do not have manufacturer certifications, and might not intend on getting them either because they are not eligible due to lack of tech or budget. These are a decent shops, usually organized but not exactly eat-off-the-floor like Penske shops. They'll save you your deductible and might have a few rebuilt salvage cars to offer as rentals to make more money from the insurance company.
Then there are the low level mom and pop, or just pop shops where there is like 1 - 3 people working. These are basically hole in the wall places. There is no office staff, just the owner who is usually wrenching will be my point of contact. They might be fixing cars outside as the shop is too small for more than 3 cars and their paint booth looks pretty rough. Places like these are usually messy, boxes of opened parts, cores lying around, dusty fenders and crashed parts leaning against the shop wall taking up space needlessly . Leaking air lines, oil spills, drab interiors, there might be an vintage diagnostic machines in the corner. The office is a mess (if there is one) and it's possible there is insurance fraud going on. It's always fun visiting these places and seeing the weird stuff going on inside.
This being said, I have seen decent quality work from the lower end shops as well. Is it guaranteed like the first 2 levels? No. They can't achieve the OE standard of repairs that a fully certified shop with the best equipment will. If you have a taxi that needs to be banged out for the 23rd time, sure, these are the places to do it and they might have it done by COB. You need a need quarter panel on your A8? Wait a month if you are lucky but the work will be top notch as these ALU parts are only sold to certified shops and repaired by a guy named Fernando who used to assemble Ferraris in Maranello.
It's really up to what your standard is for the level of work you need done.
He called and asked me to come down so he could show me something on my heads. I followed him through the maze of engine parts,past piles of valves,springs,pistons etc to my heads.
I love going to shops like these. It's like a museum or being in a movie, or in an American Pickers episode. You can't replicate this environment, it has to be created by a slightly OCD or ADD mechanic over the span of at least 2 decades.