Not to worry.
Unless you go way wrong, your warranty is still valid. Your first check, Run in, is just a glorified oil change so it's fairly cheap. The Dealer can check for fault codes or anything unusual and while you're waiting, pick up another filter and oil if you like. The next inspection, 6000 miles, ia a repeat of the first so should be the same cost. It's the 12 000 inspection you really need to consider. It requires a valve clearance check. There's an excellent write up here on how to do it as long as you're confident in your abilities. Should your engine blow up and it's attributed to incorrect clearance then.....all bad. Also consider, the valve clearance spec changed to a higher gap recently and depending on your build, may have been set to the old spec and will require reshimming which, since you're asking, I will assume you're not going to pull the cams etc yourself to accomplish this. (all in one sentence
My advise, Dealer for the first, change your own oil at the second, Dealer for the valve check. See where you are by the next valve check at 24k miles as far as warranty and confidence goes. Near the end of the warranty period have it checked for software updates or recalls.
Having said that, I bought two GS's and never went back. Bought a number of filters and oil and filed the bill. Mine's out of warranty now and she wrote hers off 3 wks ago
Service message? Who cares!