Crank AND rods are different. If the 4.8 used the same rods as the 5.3, then the piston would be far down in the hole. The 4.8 DOES have flat-top pistons though, compared to the dished pistons in the 5.3. Now besides the piston volume, they do have the same dimensions. So you could swap a 5.3 crank/rods into a 4.8 or swap 4.8 pistons into a 5.3 for a 10:1+ compression 5.3. Been done many times...
For the mating an LSx engine up to an older transmission situation, here's how it goes. If you have an iron-headed '99-00 6.0L, then you have a long crank snout and you can bolt up any old trans without issue. If you have an '01 up 6.0L or any other LSx(4.8, 5.3, LS1, etc) then to bolt up to a older trans you have a few options:
1) Run a factory LSx dished flexplate along with a crankshaft pilot extender.
2) Run a crankshaft spacer and flat flexplate combo from a '01 up 6.0L that was backed by a 4L80E.
3) Get a custom made torque converter for your trans with a LS1 style front cover.
If I go with the overdrive, I already have a 3.42 rear I can stick under the back of the truck.
