We have road tiles (straight road, corner, etc) that we use as tiles to draw our road. We never had any gaps or seams because Spine filled the padding around each sprite as if it was clamped. So a straight road would have it's padding filled with the road texture at the top and the bottom, and transparent pixels at the sides.
I don't know when it changed, but when updating the atlas it stopped doing that and I can't seem to get the old behaviour back. The current version doesn't fill in pixels and causes seams to be visible.
Am I doing something wrong or am I missing a setting? I've checked our old atlas texture and they really did have a filled padding around the image (e.g. the road had 130px visible road when the source texture was 128px high).