I've put together four ARs and had no incompatibilities. Never had FCG pins walk out either, including a fifth lower I completed recently. As long as quality parts are used and you select the right parts for your configuration I wouldn't expect issues.
As far as warranty, that's not been an issue either but it's a good point if something does go wrong. To me, in order to get exactly what you want it's a slight risk worth taking. Now if someone slaps together a cheap, poorly conceived thing, then a $700 factory AR makes more sense.