No, they are not used in the same contexts. They are quite specific: "so be it" - This is used to say something like "I accept that this is the situation". There is an implication that you are not happy with that situation. "let it be" - This is used to say something like "Don't interfere". It is an instruction or suggestion to someone. "have your own way" - This is used to say "I accept your opinion / decision'. This is often a way of ending an argument. Although the first and third are similar, the contexts are different. In the first, you typically don't have any say in the situation, whereas in the third you do, but you are conceding to the other person.

so be it or let it be are same like: st1: i must do my homework. st2: let it be for tomorrow, or so be it for tomorrow. and have your own way means follow your own policy. Like: st1: i should know how he passed the examination? st2: let it be, have your own policy if you found more than this please inform me

Gary’s answer is good but I want to add that in the US, we wouldn’t say “Have your own way” (though we would probably understand it). We would say “Have it your way.”