The differences between the Pack Covers come down to the fabric they are made of and their intended use.
The Nylon Pack Cover is made of 70D PU-coated Nylon and is available in three sizes (S, M, L). It is a great choice for most hikers and backpackers. It is contoured/tapered to fit snugly around a pack.
The Ultra-Sil Pack Cover is made of 30D Ultra-Sil and is available in four sizes (XS, S, M, L). It is lighter than the Nylon Pack Cover (4oz/113g vs 4.9oz/139g for a size Medium) and would work well for someone such as a thru-hiker who intends to use the product on an extended, frequent basis. Sizes S, M, L have a keeper strap to pull across your pack harness.