Are you sure that it's just the order of the props in the actor file which defines which is above? I had the same problem with my olive mill and changing the actor file didn't solve the issue, it just appeared different each time.
I think instead of or additionally to blending out at the edges, you should cut along the gaps between stones. You could avoid the triangle stones at the edge of round decals for example. Also I think you should scale the tiles down, they are too dominant imo.
To easily edit it I strongly recommend using masks in the material node shader if you're not doing so already.
Well, a resource cap, with dropsites increasing it, is an interesting and not complicated idea, as long as it’s not too disruptive and only penalises under-building dropsites. Loot can be calculated as some fraction of total resources, divided by the amount of dropsites. Something I was thinking is that CCs are given too much importance as dropsites, and this just comes from other RTS, but it’s historically inaccurate (when compared to the other specialised dropsites), and causes fields to end surrounding it. Of course the idea is to have a dropsite at the beginning, but I wonder if, while one progresses, adding some penalty to them, or some bonus to the other dropsites, wouldn’t restructure things to look better, or maybe something else is better, with those consequences in mind. I have other ideas, but are more radical.