With means 'accompanied' or 'by'.
In means 'enclosed' or 'surrounded by'.
Method overloading is calling what appears to be the same function in a program but - because different arguments can be given to the function - it is technically a different method being called. This concept of multiple methods that are the same is known as method overloading.
Varargs is shorthand for 'variable arguments' and is a way of passing a set of arguments to a method without explicitly identifying each individual argument.
Putting it all together:
1) Method overloading can be performed by (using) varargs. So 'method overloading with varargs' is fine.
2) Varargs and method overloading as programming concepts accompany each other. You use different arguments for the same named function in overloading. You provide different arguments to a method with varargs. So 'varargs with method overloading' also works.
3) Method overloading does not need to involve varargs. You can overload a method that takes only one argument instead of a set for instance. These other implementations suggest that conceptually method overloading is larger than, and encompasses, varargs. So 'varargs in method overloading' is correct.
You should not say method overloading in varargs. They can't enclose each other.
I would suggest that all three of the above are perfectly valid. Of them perhaps 2) would generally be less used, but in the context of your question, is absolutely correct.
I would choose You misunderstood because, as you say, this is an action that happened in the past: it happened when that person interpreted whatever. Besides, it sounds more polite to say You misunderstood (you made one mistake) than You misunderstand (you continue making the same mistake).
As for your second question, it does not sound unnatural: it is plain wrong. I don't know exactly what you were taught, but you cannot construct the future tense using the past tense. Of course, if it is something that could have happened, you would just write:
Since Bob is not a native English speaker, he surely misunderstood
the meaning of the letter.
Best Answer
"X's murder" is an informal or colloquial construction: it may stand for either the murder of X or the murder committed by X, so it is up to the user to make sure the ambiguity is unimportant in your particular context. Agatha Christie's book The Murder of Roger Ackroyd does refer to him as victim, but a whodunit reader might consider the possibility that he was actually the killer...
Note that in a very formal context such as a court case, 'the murder of X' is correct (assuming that there is no question of accident or suicide) but 'the murder by X' assumes not only that X is guilty but that he has committed no other murders.