I seem to have missed your first post. It is hard to say without seeing the close up of the leaves, but I would lean towards leaf rust as well. I had a constant battle with rust when I was growing in Houston. Leaf rust can cause a tree to defoliate. Between the heat, humidity and leaf rust, I'd have several trees which spend the summer defoliated. As temps cooled towards the end of summer, the trees behaved as if they were breaking dormancy. Being in a humid environment helps the fungus multiply and spread. If you catch it early enough, just clipping and disposing of the few infected leaves could help prevent a bigger outbreak. The key is to get rid of the infected leaves.
I have found several common characteristics of trees when the roots become constricted. First, the growing limbs seem unnaturally thin. Kind of like a body builder who works out the biceps and triceps but forgets to work out the forearm. Also, the space between nodes shorten... sometimes significantly. Thirdly, the tree does not produce a lot of leaves. Fourth is more fruit than you would expect given everything else that is going on. Based on your pictures, I'm not sure the tree necessarily needed a root pruning, although it will benefit from it.
I'm glad you pointed out the thick mat of roots at the top. I think this mat of roots is not only indicative of watering issues in containers, but also is a contributor. I see two problems with this mat. First is the density and tightness of it prevents water from trickling through it to the mid section of the root ball. Second, since it is exposed at the top of the container, it is more susceptible to temperature fluctuations. Since this is where a majority of the moisture/nutrients are absorbed by the plant, the plant suffers more on hot days... when it needs the moisture for transpiration. I have found that mulching the tops of containers worsens this problem since the roots want to grow into the mulch (path of least resistance).
I would not worry too much if there is only couple of inches of water logged growing mix at the bottom. All growing mix have perched water. It is where the equilibrium is between the growing mixes desire to hold onto the water and gravity wanting to pull the water down. Lighter growing mixes have a shorter perched water area, while denser (growing mixes in SIPs) have higher perched water area.