I know lots of people still riding on their R550s with no problems, myself included. I was 110kgs when I rode on that set of wheels, its coming to 4000km old now ... no problems.
I think that factory wheels being factory wheels will not have been individually checked over, and the overall build/inspection will not have been as high as a handbuilt wheel.
But if you look at the design of the R550, and the mavic factory wheels, they have eliminated a weak point of tradition spokes by having spokes that are anchored at the rim, and just a straight pull design. These spokes dont have an elbow, which is where most traditional spokes break. Also the higher end / newer models are built on a off center rear rim, which would give a more balanced spoke tension between the drive and non-drive side, thereby resulting in a more reliable rear wheel.
In my opinion, if you take a set of factory wheels, and get someone (or yourself) to do a QC on the spoke tension, and true the wheel properly to begin with, they would make quite a reliable set.
I have only built two wheelsets (14G spokes 3X), and also trued my R550s, and they are all good. But if I had to choose between the wheelsets to take on a 200km ride or on a tour, I would choose my 32 spoked wheelset, simply because if the spokes broke, replacement is relatively cheap, and more importantly easily found. Also for the Paris-Roubaix race, many pros go with the 32 spoked 3X wheelset for reliability and "comfort" (relatively speaking).
I suggest reading up on basic wheel design and the stresses a wheel faces. This will help you to put into perspective some of the things you read on these forums, and what the bike shop will tell you.
With lower end wheelsets, sometimes the rims are so badly manufactured, they are just impossible to true and still maintain a consistent spoke tension around the wheel. With such wheels, there is nothing much you can do but ride until they break and then upgrade.
To address your concerns about "skinny" wheels vs MTB wheels. Chances are that the flat-bar roadie you get will have enough clearance to mount 700X28C tyres or even 700X32C tyres. These wider tyres should give you more comfort on your ride, but will relatively faster than your MTB ones.
Just out of curiousity, why are you going for a flat-bar bike? I can speak from experience, that I went with a flat bar, and it wasnt long before I got hooked, and went to a road bike. In hindsight, the flat bar only served to get me hooked on cycling, but I should have just done a road bike straight away.