1. APU's you are right can only be paired with certain graphic cards however, that being said once you get beyond the 200 dollar range you will have far better performance with a discrete graphics card then trying to match it with a card to get there duel graphics configuration.
2. Its not ideal mainly because if you had plans to go with a discrete card you would go and get a different platform whether it was a AMD FX or Intel i5 you would get something else. They are directed at a completely different audience for people who just want a onboard graphics card and a system that works a very entry level gaming machine.
if their main concern was to target those people who are only after the onboard graphics then why would they include extra PCIe? I mean, it should have a purpose right? so FM2 A85 series of mobos that has several PCIe slots are useless.
Well lets look at the a10 for example it provides a decent graphic experience and is a quad core but if someone turns around and wants a graphics card its a little hard to just say no we won't allow dedicated graphics card I believe its there so that people would still look to graphic cards if they wanted them.