I planted a Kohala Longan last year. It does not appear to be grafted. It grew new branches on the top last year, making it 5 feet tall. This year, it branched profusely near the ground. Now it looks like a bush rather than a tree. Is there any harm in keeping those low branches or should I prune them off?
The biggest concern in your climate would be dirt splashing onto the fruit/leaves during rain. This can spread disease. You have the ground mulched, though, and that helps prevent this. Another concern could be harvesting ease, with the higher plant possibly being preferable in that you don't have to bend over near as far in order to harvest the fruit or to deal with pest/disease problems and plant shaping.
In other words, lower branches cause no major concerns here, but pruning the lowest branches is your call, considering practicality/aesthetics.