Yes and no...
The bellhousing patterns will match up except for one bolt. Don't worry about it, bolt it up and go. To the best of my knowledge, bellhousing depth on automatics is the same, meaning you can swap at will, but be aware that later LSx motors have a metric TC bolt circle that won't match up to earlier TCs. The first year of the LSx (97 or 98 I forget) used an oddball flexplate that reportedly still has the non-metric circle but I couldn't confirm that. At the time I was trying to mate an early 4L60E to an LS1 which is why I discovered that little gem, but instead of tracking down a mystery flexplate, I bought a newer TC.
Manuals are different. I just went through this for a T56 swap on an LT1. As delivered from the factory, T56s behind LSx had a shorter input shaft and therefore a shorter bellhousing depth. I was told by some that you could use an older (longer) input shaft with the newer (shorter) bellhousing if you drilled the hole in the crank deeper and used a special pilot bushing, but others say that the splined part of the input shaft is too close to the crank, and it doesn't allow for complete disengagement of the clutch. Still unclear on which is the truth. I think its simply a matter of getting the bellhousing that corresponds to the length of input shaft you're dealing with.