Would it be a possibility to keep the empeg for home use as others have suggested, and build a carputer too?
You may be able to keep the dock in the dash just in case you still want to use the Empeg in-car at a later stage.
It sounds to me as though you are pretty keen on the carputer option, and you make the valid point that if something inside fails then it is relatively easy to replace e.g. memory, PCI cards or mobo, just slot another one in.
As mentioned, the UI is not as good yet as the Empeg, but if you put up with this for a while, no doubt it will improve with upgrades.
As far as S/N, frequency response etc. goes, I second Bitt. In a moving car the background noise will overpower any circuit noise.

Just my 0.02