It's a matter of preference. For yard planting in frost free areas, branching higher is nice, as it allows one to walk beneath their trees. My personal preference is to branch my mangoes at a height of roughly 4 feet, which allows me to have the yard covered in trees but without losing the ability to utilize the space. Keeping total tree height to about 15 feet gives a good amount of producing canopy which is also low enough to harvest easily with a cut and hold pruner.
Low branching is not necessarily a problem with fungal infection, as the producing part of the canopy will still be 10+ feet up in just a few years, leaving only bark in the lower sections as the lower canopy is shaded out. My bigger keitt mango tree, which is probably 30+ years old, has a gigantic (> 1 foot thick in diameter) branch that is about a foot off the ground. It makes a convenient bench :-).