There are a few subtle items...
Package 1 @ $1538 list the lens separately as shown below:
EF 28-135mm f/3.5-5.6 IS Image Stabilizer USM Autofocus Lens
E-72U 72mm Snap-On Lens Cap
Lens Dust Cap E (Rear)
1-Year Warranty
So likely the OP is correct in that the lens and body are packaged separately (note rear dust cap). But more importantly, if it matters, is the lens is likely a gray market lens; note the terminology of 1-Year warranty. The body in the same package is shown as 1-Year Canon U.S.A. Warranty.
The $1638 package simply states 1-Year Canon U.S.A. Warranty as the last line item and no separate rear lens cap is listed. Hence it likely applies to both body and lens.
If I was buying, I'd go for the cheaper package. The lens warranty doens't mean much and that isn't the greatest lens in the world anyway and likely to be replaced by anyone knowledgeable.