You can look online at what the upgrade parts cost. If you were upgrading to the AMD main board you're looking at $450-$700, versus $1200-1550 buying it new. The Intel i5 components are similar but i7 are a bit more expensive. Thus far they have been consistent about releasing upgraded components. You are locked in to buying from them though - so if they stop releasing upgrades you're out of luck.
If you don't need the latest and greatest, going used is going to still be a better value proposition.