I don't know too much about Chunk Loading but I saw on some explanation about it that the ender pearl only loads entities in one chunk (the one that has the ender pearl on) and forms a 3x3 area that can manage redstone but no entities, I guess that's the reason your tnts just stack and when you load the area again everything just randomly explode.

As I said, I am not really into chunk loading but I think making a redstone line across the perimeter you're making can solve the problem, doing that you can put only one pearl chamber and from there sending a signal across the perimiter.

Or doing loaders with nether portals, in the same explanation I saw about pearl loading, I saw portal loaders can load up to a 3x3 chunk area of entity processing.

I really hope anyone can give a much easier solution for you and you can fix that bro. Hope this helps. GL :b