One of the major advantages of buying a new bike is nothing is worn out. With a used bike you have to take into account the need to replace wear items: chain, cassette and possibly rings, as well as bar tape and brake and shifter cables. That does not seem to be a problem in your case, but I'd want to very strongly verify the 50km claim.
The other benefit of a new bike is getting new technology: 11 speed compact drivetrains, disc brakes, through-axles, internal cables etc.
Plenty of people ride bikes with rim brakes and QR hubs, and you may be perfectly happy with disc brakes. One upgrade you'd get with a newer bike that I would seriously think about is an 11 speed compact drivetrain, which will give you more range of lower gear ratios. That may be useful to you as you start out on a road bike, especially if you live in a hilly area.
Another feature that newer bikes tend to have is clearance for larger tires, and slightly wider rims which give the ability to run 25mm or even 28mm instead of 23mm or narrower.
A benefit of the older bike, especially a highish-end bike like the Madone 5.2 is it will be much lighter than a new bike bought for the same money.
Another advantage is you'll get a threaded bottom bracket which wont creak like a press-fit bearing one :-)