First, flattop receivers are really only necessary if you are mounting *magnified* optics, or if you must have the ability to swap sights and optics all the time.
Reflex-type sights (Trijicon Reflex, AimPoint, etc.) are designed to work in concert with iron sights, and work great with fixed-handle uppers. You can duplicate this setup with a flattop, but it will cost you a lot more money and won't be as secure.
The advantage of flip-ups is that you can keep them mounted on the gun, but out of the way, for use with magnified optics. That way, if your optic breaks, or you need to remove it for some other reason, you've got iron sights available. Most solutions are decent, but not quite in the league with fixed sights in accuracy and durablity. And, they cost a lot. But they do provide the best combination of magnified optic and iron sights.
Anyway, like any decision, you need to figure out your requirements FIRST, then pick the hardware and configuration needed to accomplish them. And any given configuration is a compromise, so you have to set your priorities.
For myself, reliability and light weight are high on my list, so I don't add things to my rifles unless they add significant value while also not affecting reliability. Other folks like to bolt every possible thing they can find to their rifle, making a 15 pound "wundergun." Nothing wrong with that; it's just a reflection of different priorities.
Oh, and [url]www.gggaz.com[/url] is one of the better places to look for flip-ups and mounts.
-Troy