Thank you for your kind explanation.
I understand one of your example "He will/won't be there now. He will/won't have been there then." well, but what makes me puzzled is you use a sentence like these with a past indicator, "yesterday."
In the titled sentence "John will have arrived yesterday", does it means something like this; "I'm sure he arrived yesterday"?
I still wonder, as a non-native, if I can use this kind of expressions someday!
Yes,exactly - I'm (pretty) sure he arrived yesterday. Read 5jj's examples again to see when you would use this.
I'm not a teacher, but I write for a living. Please don't ask me about 2nd conditionals, but I'm a safe bet for what reads well in (American) English.