Your arguments are not valid. If you get a machine with an AGP slot, you can put any AGP card in you like, even if it also has onboard video. In fact, modern chipsets detect the card and turn off onboard video automatically. But you can find top notch boards without onboard video.
Onboard sound/NIC/etc. You get PCI slots on your motherboard. You don't get fewer PCI slots just because there's onboard stuff. Onboard stuff is just a bonus. You disable what you don't need. And it saves the company money to make just one board, rather than several versions. Which means it is cheaper for you to disable what you don't want than it would be to buy a custom board with the parts removed.
So you "like to have the flexibility to change out a new sound card or video card" is not a valid argument, since most boards have an AGP slot and several PCI slots for adding whatever you need, and whatever you don't need can be turned off in BIOS.
In fact, the onboard stuff increases flexibility. For example, I used my newer system as a second system for a while, with onboard audio, before retiring the older system and putting that sound card in the newer system.
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