Top is not fungus, looks like you are having root issues. Shriveled and dark areas on the trunk are very bad signs, it's almost assuredly not going to make it. Bottom pics seem to tell the same tale, with maybe a little more hope. You cut it back/down as the top died off, right? My guess is the roots don't like whatever medium(s) that is you have them planted in. If I'm right, those new growth shoots (which do look to be part of scion, not the rootstock) might develop, but the tree will continue to suffer and any new growth will die.
I would reassess your potting mix. You can try and save the bottom one by replanting it in a new potting mix, you'd have to act fast, but you really need to get your potting mix figured out before you put more time/money into mangoes (plenty of threads on here about what store-bought or homemade mixes work well). Seedlings are pretty resilient to whatever they are planted in and the amount of water they are receiving, you'll think they are happy, then after the first year or so they'll start displaying signs that they are not happy. It can look like anthracnose or some other fungal issue, but it's usually your roots.