if you read the story of Dhul Qarnayn carefully two things are obvious is that he is powerful and is traveling a lot. God gave him the authority to treat people however he wanted. There are two mentions of the sun. In verse 86 the word maghrib is used which means the sun is setting. Also it says wajadaha which means he watched or it appeared to him. Until, when he reached the setting of the sun, he found it [as if] setting in a spring of dark mud, and he found near it a people. Allah said, "O Dhul-Qarnayn, either you punish [them] or else adopt among them [a way of] goodness." You only quoted part of the verse. After he reached the place where he watched the sun set he was allowed to either punish or treat them good. In the next verse he says that if they are bad and transgressors we will punish them and if they are good they'll be treated with a good reward. Then he went on his way again 18:90 - Until, when he came to the rising of the sun, he found it rising on a people for whom We had not made against it any shield. The word is matla3 al shamsi which is the sun is rising. First it was setting, now it's rising so he was probably walking for at least a day. Does this mean that the sun was actually rising above the people? It's called perspective. It's telling you how it appeared to him, please use your mind a little.