It's the same material. i believe the difference, the parts that makes the material repel water, is probably some polymer coating. Take a look at side by side comparison of Tom Brady alternate elite jerseys. The jersey on the left is a pre-made unit from the Patriots Pro Shop 3 seasons ago and the jersey on the right is a custom from Fanatics that I just received.
The left jersey repelled water and the right jersey absorbed it. Quality wise they are about the same.
What about the numbers? I remember seeing in this thread someone showing that the fanatics customs use the reebok numbers (layered on top of each other) compared to how Nike Elite numbers are (white base with the borders stitched around). But that was couple seasons ago so it could be different now.
Thinking about getting a white Gates jersey