I dont know much about the differences from the DE and DET blocks and/or heads, but is very common for two engines with the same basic block (one Normally aspirated, one Turbo) to be different. Usually the difference involves coolant passages, oiling systems (more oiling at certain areas), and sometimes reinforcements to the block itself. Starting off with a DET engine would make everything a lot simpler and most likely cheaper, because if you have to do a lot of machine work to a block, it can become decently expensive. Its like buying a car; buying a car all put together is cheaper than buying all of the parts individually to make the car.
Just a side note, the ideal engine block to build a high-performance or race engine would have around 60,000 miles. It was found out in the 60's and 70's by some astute race teams (Penske was one, as was Donahue and the brillaint engineer that worked with him whose name I can't remember right now) that blocks with that many miles produce more relaible power. It has something to do with the way that the metal has aged and become stronger with all of the heat cycles. BMW used 60,000 mile used 2002 and 320i engine blocks as the starting point for all of their insanely powerful (1200hp+) turbocharged formula 1 engines in the 80's.