Ok. I'm in front of my computer now.
Until you realize the "reprogram" is nothing more than checking a box that you can do yourself with a $60 bluetooth module (or many other systems).
In your case, it was likely already checked as you actually had the system, it was just missing a part/faulty. Even in that case, parts *are* available separately. Most parts guys are too lazy to look into it though. And, it wouldn't affect warranty whatsoever. With something like this (with VAG anyway), it's impossible to tell if the OEM system was installed at factory, port, dealer, or in bob's garage - assuming it was all installed correctly. With my last Ram, after I added all the nav, and premium instrument cluster and such, all I had to do was make a phone call to get them "added" to my VIN and they were all covered under warranty as well. I'm sure each manufacturer is a little different.
e.g. - My TDI Touareg I had a few months back. I snagged the OEM hitch from car-part, and bought the module/harness from the dealer. Cost me $350 or so and a couple hours of my time.
Now, I'd venture to guess most independent shops can't handle this efficiently or accurately. You've got to find a specialist. But guess what? Most dealers can't either. Majority of dealers are chock full of broom techs with access to a 1-800 tech hotline number and a large dealer bankroll that can afford to pay for all their mistakes. Most techs that stick around long enough to attain master status, don't stick around much longer because they're tired of training car wash kids to work on 100K sedans. However, if you have work performed there, you've got security in that large bankroll behind it so they'll hopefully make anything right. The last dealer I was at had a $12,000 internal service "policy" per month. Anything the dealer had to "eat" came out of that policy. It was maxed out and beyond most months.
To expand on that a bit. You take your car to the dealer for a check engine light, you are out of warranty. You know that survey you always get after work at the dealer? That is SERIOUS business to dealer employees. Their pay depends on it. So, the big question that matters to the tech is "FRFT - Was your car fixed right the first time?". So, let's say they pull multiple codes from your computer. Oxygen sensor, MAF sensor, fuel trim errors, misfires, and a catalytic converter fault. You can just about guarantee that kid that was washing cars 6 months ago is gonna tell you that you need about $2500 worth of work including all those sensors, cat, etc.. He's likely also gonna list questions on his estimate like timing belt? pollen filter? air filter? - directing the service advisor to examine your history to see if these items have been tended to. However, the service advisor was also just washing cars 6 months ago, so he's just gonna try to sell you those services too. Oh, but you should also get this fuel induction service. And this power steering and brake and coolant flush. And all these other snake oil packages. So, now you're $4000 into it, but your car was "fixed right the first time", so they get paid. Except, it wasn't. 2 days later, your light comes back on for the vacuum leak it originally had causing all those faults. You take it back, they blame it on something, but go ahead and eat it on good faith. And maybe throw in a car wash and oil change for free. Congratulations. You cost them $80. They took you for $4000. But somehow, you come away feeling ok about the whole situation. This happens Every Single Day at most dealers.
Not bad enough? How about labor times. There are industry standard guidelines for how much labor should be charged per job. I've never seen a dealer use them. They short staff so much, honestly, most don't have time. And technicians? They get "burnt" so bad on warranty times, customer pay jobs are "redemption" for them. Let's say you have a faulty oxygen sensor under warranty, the tech gets paid .60 hours or so to replace it. It's hard to get to. It took some extra diagnostic time to figure it out. First time he does it, it takes him 2 hours. He lost money. So, next guy comes in out of warranty and needs the same job performed. Well, industry standard usually pays more than factory warranty time, let's say it's 1 hour as opposed to .6 Doesn't matter. He lost his ass last time under warranty, so he's charging you 3 hours. That's why Julians brake job quote was so outrageous. There was probably 3 labor hours quoted + parts (not to mention the way dealers "matrix" parts prices - all parts prices are OVER retail at dealers now, thanks to a bean counter with no scruples). Don't believe me? Go look through your glovebox at an old invoice where you had work done at the dealer and google the part numbers and compare prices. Compare to OEM MSRP which is easy to find. You paid more. Sorry. Want more proof? Get an estimate from a dealer for something. Call 3 other dealers and get quoted for the same job. I bet every estimate you receive is different. Had nothing to do with industry standard anymore, it's all about how greedy they are. When you call for an estimate on a repair (not maintenance, they have menus for that), the advisor will put you on hold because he has to go ask a technician how much he wants to do the job. YES. HOW MUCH HE WANTS. Are you freakin kidding me? That's how broke our system is right now.
However - on the other side of all that. If you're the guy that hates money, and always has the dealer fix everything they recommend to you, you have some awesome leverage. Take for example the 2010-2013 Audi's the burned more oil than gas. If you were out of warranty and needed new pistons, and you were a good service customer there, the dealer would go to bat for you, and very likely get your repairs covered under "goodwill". So, you might've spent $5000 more than you should've on repairs and maintenance for 3 years, but you just saved yourself a $9000 repair bill. It doesn't always work out that way, but it does happen.
I'm obviously jaded a bit, but I'm kinda passionate about it. It took me years to leave the dealer because of my love for the brand, but I just couldn't deal with the way most do business anymore. I tried fixing it multiple times, but bean counters determined it was more profitable to do it their way. If I didn't have such passion for resurrecting the unfixable, or fixing what noone else could, I would've left the business long ago. There are good dealers out there. There are good shops out there. But it's gonna cost some of your time and patience to find em.
(about 10x the price of a standard set w/domestic parts?) 
