The thing is I don't want to ground layer if I these roots are going to get thick again because I need more trunk development and healing.
One can remedy thick/heavy roots by pruning them hard when repotting the tree - the more smaller roots you get elsewhere, the harder you can prune back the 'big heavies'.
A thing to keep in mind is that roots will grow most strongly below the branches with the most foliage. Suppose you cut all the branches of one side of the tree. The roots on that side will become weaker over time. The others, on the side with branches, will get stronger. This tendency can be combatted, though, by root pruning.
I would only be thinking 'ground layer' if the roots aren't on the plane of the final planting surface. Unless your tree is perfectly symmetric around the trunk, it is inevitable that some roots are going to get bigger than others over time.