你不是要回家吗 = Is it not that you wanted to go home? vs 你要回家吗 = do you want to go home? As in English, there is a difference in subtlety. So you can say the first one is somewhat impolite compared to the second one.

都可以表达一个意思，只是情景不同表达出来的意思就略有不同

不是……吗 doesn't definitely make a sentence impolite. If your conversation with a native Chinese speaker made you wonder, you may want to know that in general, confrontation is impolite in the Chinese context. "didn' you say you wanted something" is confrontational. Mentioning "go home" as a host to your guest is considered impolite, too.

你不是要回家吗？ = 你要回家。 because you said or you need to go home