Okay, solved from another forum. Posting solutions here in case someone else is wondering.

1. If you use Filters > Map > Bump map, you should be able to bevel the cobbles without affecting the border of the layer.
1a. The GIMP Decor > Add Bevel filter has an option to create the bump map for you.
2. Create base pattern with no textures (example: 600x600 image). Double image in height and width (ex: 1200x1200). Fill with 4 tiled copies, add texture and cut the middle 600x600 section as your pattern.

- Ernie