Does Erase-then-Copy defragment as it transfers?
 

If I copy my entire computer to an external drive, then restore the whole thing back to my computer, I know that the result will be bit-for-bit identical.

What I'm wondering is, will the HD be better optimized? That is, does the performance of the internal drive improve (faster seek, read, and write times) because of less fragmentation and more contiguous available space?

Yes. See the Fragmentation white paper (available from the SuperDuper! page on this web site).