As a motorcycle mechanic my self I would be more concernd about them scratching the paint. As a rule at the places ive worked everything gets an extensive test drive, rules being take it to 100mph, hard cornering and braking making shure everythings ok, any majors ride for half an hour. bring back to shop and check all important componets and fastners. After Im done the service manager goes for a 15min ride to check as well. I was told by the service manager, if you screw up its better you die rather than a customer.
Personally I would be more concernd about getting a tire change on a bike, its a simple everyday operation that a mechanic doesnt give much thought to . When you do a total rebuild your going to double and tripple check everything.
HD is doing what they should, fixing a factory defect.
A collision damaged frame you might have warrented concern and a insurance company would fix the bike if it was cheaper, if you didnt like it too bad.
If HD gives you a new bike, how many more will line up behind you. I dont think it will happen.
My advice to you is if you feel unsafe, take it to another shop when you get it back and have them check it over. The odds are it will be fine.
Like I said a tire change is riskier, they ussally let the apprentices do that.
I wish you luck and hope you are happy with the results.
Ride safe!!!