Hi! Could you share the meshes? Does the same issue occur when baking just one element? Is this a game asset? Low resolution per element probably doesn't help too. Since there are many repeating elements, part of the texture could be reused allowing for higher resolution. A measure to to reduce aliasing showing at seams…
Yes, stacking UVs, means you end up having less unique UV shells and can scale the remaining ones, so they have more resolution. You could have a couple of variants of an element to avoid repetition. Further variation can be added with some masks on top, either texture or vertex colour. A checker texture can be used to…