Non Toyota certified shops - I agree. I would avoid them. The Lexus service rep once told us that he didn't recommend using their own shop and that they don't use it for their own vehicles if they're damaged. It's not a pay for a sticker type certification like some manufacturers use. I think there's only one in about 10 toyota dealer body shops is Toyota certified.
But in my experience, a Toyota certified repair shop - they will be better than any other body shop - even the custom shops. I've been around a lot of different body shops. I've yet to see a single high end shop do the same quality of work as the Toyota certified body shop that repaired my 4Runner. For example - call any body shop you want and ask them about Toyota super white being single stage. They won't will believe you. They will call PPG and ask. PPG will tell them it's a base clear (which is wrong), and they'll go with that answer. Toyota shops know the difference. They will not repair with single stage, but they are trained and provided the proper products to get a proper match to the single stage. And they have very strict guidelines - like paint blend areas. There are a limited set of areas that they are allowed to blend old and new paint. So you'll never see a door blended for example. They'll paint the entire side. If the inner fender foam is delaminated - regardless of condition on the outside, they won't repaint it or repair it. 99% of shops will put an aftermarket fender without the foam internal cushion on and call it good.
And - I've never seen another body shop that will replace all the hardware with OEM. Not crap aftermarket plastic parts and clips. Toyota cert. shops do. So your panels actually fit when you're done. And they fit next year. And the year after... Custom car shops - never do. And they tend to really love bondo. Especially the hot rod shops. Toyota certified shops are not allowed to use body filler in almost any circumstance. And Toyota requires every tech to be certified by Toyota - and trains them on things like how to cut, where to cut, how to weld UHSS panels. Your local custom car shop - probably doesn't have a certified welder in the bunch and is just winging it. (We see the same from well known off road shops.)
Ultimately the point is that they have access to the best tools, they don't cut corners, and they're not cheap. But they do the repairs correctly with all OEM parts and OEM paints. They will weld with the correct steel and the correct filler rod.
