CPU upgrades aren’t available from the store configurator, but they have a few you can contact sales for directly before placing your order and they will hook you up. This was the availability and pricing as of January;
You can of course buy your own CPU, but I’m not sure they’ll sell a full build sans any CPU, so you’d have to resell the 3204. Easier to get the better CPU when ordering. The price for the 4210 at least didn’t seem unreasonable. That won’t help with transcoding though. I don’t think any CPUs for the LGA3647 socket support Quicksync, so you may need a separate GPU for that.