Diagnostic Fee at dealer

Because they can!
Those places that do it for free will hook-up a $20 OBD2 scanner from Walmart and read-off generic Federally mandated codes. It's not a Toyota specific, Techstream OBD2 code reader that will tell you specifically whats going on and enable you to toggle sensors and switches to isolate your issue.
Hope this clarify things.

 

you can do your own with an autel maxi 200

 

I recall the first time I encountered that. Forget what the issue was exactly but it was clearcut. I phoned up service, made an appointment, brought it in, got the the phone call about an hour later, something along the lines of "Yes, that needs doing. Would you like to book an appointment to bring it in?" Yeah I guess so...

 

Proper diagnostics are much more than a scan, but most people don't know better.

I'm not saying Toyota will do it correctly because that just isn't guaranteed. But as Biomed01 points out the dealer is supposed to do a lot more than the freebie places and they are supposed to use their experience to evaluate the results of their deeper scan in context with the symptoms reported.